As Shran mentioned, nothing specific happens with Effects on Cover dice, though if I determine Cover to be extremely effective I will use the E as an effective 1 or 2. remember though that the reason that Cover is variable is to represent a target popping in/out of cover in a fight and the randomness is when you catch them. if someone is entirely cowering in complete cover, never coming out you probably should make them an invalid target unless the attacker can see through walls or has a spotter or a indirect fire weapon etc.
How to balance someone with Superhuman Attributes after the fact…
First, if your game is starting out be aware that almost ever non-combat Talent tree pretty much has this effect anyway. There are plenty of different ways that PC’s will generate Extra Momentum for successes and it is something you need to be ready to deal with.
So, this is what I do.
A) If your player team start bringing out the big combat boosting abilities the threats and adversaries they encounter should do the same. The player has built their character to be successful at that particular part of gameplay so they should be expecting their enemies to confront them at that level. Same things goes for if a player purchases a TAG or a Hyper-Magnetic Railgun. These are expensive and notable pieces of Tec, their adversaries should plan to counter that. Especially if a player is obvious about their upgrades.
Now, you might be generous and have the first couple of outings of your upgraded character not seeing an increase in adversity as a result of their upgrades. but remember as a GM you should see what your players take for your character and then provided equivalent challenges.
AKA Bad Guys can make Lifestyle checks off-screen to buy stuff to.
B) Deal With It Through NPC actions. This one is less about directly opposing the trait itself and more that you can counter it by minimizing how frequently Agility and Strength based checks are rolled. As an example I would be challenging that player with making tests based off the other attributes. As others have mentioned Infowar and PsyWar attacks are great to level at those types, but you can also just challenge them outside of combat with perception rolls or have them being the one needing to do a negotiation check or a discipline roll etc.
I personally don’t like this option so much as it really is very adversarial and your player is probably not interested in those sort of challenges if they took combat relate upgrades.
C) The difficulty curve doesn’t stop at 5. D5 is not the limit of a Difficulty roll, its just the recommended limit for when a GM sets a skill checks base amount and the recommended threshold for an average roll. You can very easily go higher than that difficulty when you start factoring in environmental and circumstantial modifiers, just look at all the modifiers for PsyWar checks.
if a player has upgraded their character to be extremely enhanced in terms of their physicality make sure you start throwing those high difficulty tasks at them. They will not only keep the momentum down, but when they pass those rolls thanks to their upgrades it should give a sense of accomplishment.
D) And finally Fireteams. If you ever think your players are trouncing your NPC’s to easily with all their sweet sweet gear in combat and you want a quick and dirty way to make your players spend Momentum en masse, use Fireteams. Preferably 4 Troopers lead by an Elite. Those 4 troopers give +1d20 each as an augmentation bonus which isn’t capped to the max of 5d20 so your Elite will roll 6d20 and while they don’t get those bonuses when the Elite has to dodge (Remember without a specific called shot to a Fireteam the GM chooses the target of the attack) they can still take a single reaction per round and 6d20 should be generating plenty of Bonus Heat for the GM.
BE WARNED a Fireteam like that is a player killing machine verse characters not ready to fight at that level.
There are plenty of other way to counteract a player with this level of advantage and you’ll figure them out in time. For now I will finish by saying, look at the heat spends for creating obstacles to hinder a target and also look at how exploit works as its a great way to have 1 NPC in any scene essentially just directly add into the GM’s Heatpool.