Edit 2: I also really like your idea of Gene-Mods to increase Gene-Troop stuff. But i feel like that would make them overly used in Lategame Empires unless RP or infrastructure demands otherwise.
Since the cost multipliers for gene mods and other capabilities are multiplicative there would still be a (soft) limit. Currently we have three levels of HP boost and two levels of power armor, with the max of both being 2x the stats for 2.5x and 2x the cost respectively, so having both 2x HP and armor gives 5x cost multiplier. If we start adding things like +aim (say, +2.5% for 1.5x cost and +5% for 2.0x, arbitrarily) and +fortification (say +0.5 fort for 1.5x, +1 fort for 2.0x), stacking the maximum gene mod of all three types plus the armor gives in this example a 20x cost multiplier before we even start talking about terrain types and such.
I think the idea of the gene mod tech you're talking about would be that as an empire transitions through the mid-game a baseline of modded infantry becomes standard which reflects the advanced tech of an advanced space empire, but these are still very expensive units to build if you stack all the capabilities so you're really looking at establishing a baseline of 2-3 capabilities for your main line infantry and maybe more for elite units. Although at that point you do need to think about if there's enough gene mods to make this make sense, otherwise every late-game empire will just run the same generic boosted infantry and there's not as much flavor behind the feature.
Possibly this could be solved by considering the terrain-based capabilities for infantry as genetic modifications - you can dig out of the DB or read in
this comment I made a while ago that there are 3 infantry-only terrain capabilities which could be moved to the bio/genetic tree (we could also do this with desert capability if we're okay removing that from vehicles/statics). That would give more specific flavor to different gene-mod units besides the generic aim/defense bonuses I proposed.