there are a couple of approaches you could take. personally, i’d default to the armor customizaton rules on pg. 347 of the core rules, essentially making the players use parts and tech tests to upgrade remotes, with the same challenge levels and complications for similar/dissimilar combinations (e.g. adding a Krab Gauntlet to a Null-Zed Zond? those are parts made for the chassis, so go for it. adding an HMG to your Fanous remote? that’s gonna be tough…). i’d even consider balancing the modifications out with an increased complication range and/or qualities like “Tin-Bot with Issues” from the Nomad career table. and when that 19 or 20 gets rolled, i would strong consider temporarily to permanently disabling the buff/custom equipment–because it’s always the cool thing that breaks when you need it most.
there’s also a good post from inane imp about weapons customization that touches on the same as above but with a more comprehensive layout… i won’t try to duplicate it, you should just check it out.
lastly, i think your instinct to use the geist customization for antipodes and pets is what i would favor too. i think of geists and pets as characters while remotes are generally just equipment. your PCs might gripe about having to constantly fix and upgrade their super cool balance breaking toy, but the drakomon critical to their backstory is probably worth advancing in a more organic/XP progressive manner.