Probably the through subspace field coils in the impulse drive. I gotta re-read my manual. Assuming the impulse drive in modern shuttle craft uses a similar design launching a shuttle at warp shouldn’t be an issue for even non warp capable shuttle pods.
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That’s exactly the scene I thought about when this question was posed. 
“The Menagerie” does leave it ambigious, true. though it is heavily implied, given the shuttle didn’t start pursuing until after we’re told the enterprise has entered warp. but in “Let that be your last battlefield” a shuttlecraft of the same type stolen from Starbase 4 two weeks earlier is encountered in deep space lightyears away from that location. which suggests at least a low warp capability.
since in “The Menagerie” the shuttle is described as having a limited fuel capacity, presumably it was just not used at warp very often since it couldn’t travel very far reliably. and even used inside a starsystem, having a little bit of warp capability would make sense, as it would let you move around much quicker than on a purely impulse driven course.
having to wait to recover the Shuttle in ST:V may not have been a technical limitation so much as Chekov and Scott not wanting to abandon the shuttle (an obviously weaker and less defensible vessel) and thus their captain and first officer to the possibility of a klingon attack. especially after Kirk countermanded the original suggestion of the shuttle returning to Nimbus II to seek safety. given that we see visable warp grilles identical in appearance to the larger Enteprise’s on the nacelles of the shuttle, it is likely it was warp capable. but probably not particularly long ranged or fast. not enough to allow them to escape pursuit by a bird of prey at least.
I always thought that the TOS class F shuttle had no warp capability but it does make sense that it has at least a little bit.
In Metamorphosis, they were bringing a Federation Commissioner back to the Enterprise when they were hijacked. The Enterprise could have made the trip in seconds if the shuttle were only sub-light capable.
I rather like the “charged warp coil” explanation. Perhaps in The Menagerie, Starbasee 11 was able to charge up the shuttle before its departure and when that was used up it drifted back into normal space forcing Enterprise to return for it.
and in “The Galileo Seven” the shuttle is launched, from all appearance, several hundred AU from the quasar, yet the Class-F shuttle manages to reach a planet deep within the quasar’s accretion disk in far less than an hour (going by dialog), indicating superluminal velocity.
and i don’t think that the idea of it using some sort of battery power makes sense… given that in Metamorphosis shuttles are clearly stated to be powered by a Matter/Antimatter reactor. i find it more likely that it does have a full warp system (most likely maxing out at warp 2 or 3)… but limited fuel supply, meaning that the range is limited.
Many TNG shuttles explicitly have warp capability.
TOS shuttles having limited warp is the only way to explain certain plot points.
I think simply allowing low warp for TOS shuttles is the best solution that doesn’t break anything.
During TOS a ship could travel between stars on impulse, it was slow but still fast enough to allow the Romulans to attack and destroy several outpost in several star systems with only one ship during a short span of time. But that was in the 1960s, when knowledge of the huge distances in space (and Einstein’s theory of relativity) were not common knowledge.
actually it is more likely that the 23rd century bird of prey was just unable to use warp drive while cloaked, and when cloaked was restricted to impulse engines only if they didn’t want to be detected. possibly even limited to using their impulse engine’s reactors as the ships main power, given scotty says their power is simple impulse, not ‘their engine’.
and we know the romulans had warp drive, given their warbirds and droneships in the 22nd century.
even if the ship lacked a M/AM reactor, it is likely it could still do warp, given that you should be able to generate warp plasma using fusion reactors (like used in a impulse engine) just at a lot less efficient rate. it seems likely that Cochrane’s Phoenix used fusion of some sort. if they had trouble getting enough titanium to build a cockpit, getting and storing antimatter seems improbable.
Sorry, but it seems that there is a misunderstanding. I wrote how things were imagined during the production of TOS and not how those inconsistencies can be explained now. If I remember correctly TOS stated that the Romulan Wars were fought using impulse drives and not warp drives. In “The Cage” it was hinted that the warp drive was relatively new, but that was before the introduction of Zefram Cochrane of Alpha Centauri as the inventor of the Warp drive in season two.
So, what does that mean?
Star Trek is always changing. If you want to play during the TOS era with the TOS look and feel, then you don’t have to add a warp drive to a shuttle. For that era an ordinary impulse drive has some FTL capabilities but is still slower than warp. But if you want your campaign to include all bits of lore introduced later, then not every shuttle has warp capabilities, those without need a warp sled (as shown in TMP).
the episode never said that though, just that it was fought with primitive ships, with lasers and nuclear weapons being specifically mentioned as well. no mention is made of warp drive or lack there of.
the fact that the BoP in the episode was operating on impulse only has falsely been taken as evidence that the romulans lacked warp, despite the fact that the romulan ships has very prominent warp nacelles. (and an earlier draft of the script actually drew attention to that fact, by having spock comparing them to an older federation ship class and then Stiles speculate on romulan spies within the federation… which was evidently meant as a set up for Stiles’s persecution of Spock when the romulan captain is seen, as the following bigoted referenced to spock being a ‘secret romulan’ were kept)
follow on appearances in “The deadly years” where a fleet of BoP’s manage to pace and attack the Enterprise when it is passing through romulan space at high warp support the idea that the romulan ships are capable of warp travel.
given the sheer distances involved in an interstallar war, across dozens if not scores of light years, the romulan ships would by necessity have to have warp drive. particularly given that earth did have such drives at the time (as the SS Valiant had such years before said war), and a war with a sublight limited opponent would be decidedly one sided.
and given that in TOS the nature of tech is left vague, we do not have to resort to “impulse can do FTL” when “these ships have warp drive” is a self evident explanation that far better fits both the dialog and occams razor.
nor do you have to reject non-TOS continuity to play a TOS era game. including material and references for that era that was introduced in later series, or which existed in preceding series, can only enhance the setting and the game play, opening up options for storylines and events far beyond what TOS alone could provide.
Another game system solves this problem with having “tactical warp” and"strategic warp".
A ship with tactical warp can maneuver and change direction while at warp.
A strategic warp ship can travel from point A to point B at warp speed, but the warp bubble is either too fragile, or takes too long or uses too much power or whatever to be tactically useful. During combat such ships are limited to sublight.
The Romulans, in this setting, had strategic warp capability but not tactical warp during the Earth-Romulan War. If I remember right Earth started the war that way, but developed tactical warp capability, a major factor in the winning of the war.