FTGU isn't "era" specific, it's pick and choose of the best parts of all era's for the tech tree, so you wouldn't gain (or lose) anything by progressing.
this is totally true.
Though your way is way complicated than it should be. You see heroes spawn true story scripts, and if we leave those out for the specific GC (FTGU in this case, where we don't even write them since there is no era change) then there will be no heroes spawned. that's why there can be single era GCs, since there is no command on era change to begin with, but even if there would be, nothing would happen to the hero rooster unless it's coded in too.
This is also the reason to why there isn't any hero change in the minor factions between eras, because they can't have story scripting(sad as it is).
Though I don't think the team would consider it, since FTGU is as TlMiller said before me, a jack of all trades GC so to speak, and limiting either the Executor or the Sovereign for the remnant wouldn't make justice sine the NR has the new classes and the Viscounts(without limits since AI don't give a thing about them) and the Hand has the Phalanxes and Syndics. And if you play PA, you also have the Preators and will have the Bellators too, so it would be a real disadvantage for the IR to lose these.