You can't balance for all maps.
Sure you can.
Map choices certainly changes the game, but its very much still FAF.
It mostly just emphasizes a different stage of the game. Turtle maps tend to emphasize the late game. Large open maps, the early game.
A problem on a turtle map is likely to also be a problem in the very late game stages of 1v1 games.
If you stealth nerfed T3 static arty for all factions but one, the first people to notice would be your Gap/Isis players.
If you nerfed the mantis, gap players might never notice... but the ladder crowd would lose their minds.
The notion that they're somehow completely different games is just wrong.
Striving to balance all maps is effectively the same as trying to balance all stages of the game. You're going to wind up with a more balanced game if you take all maps into account.
Think of turtle maps as "canaries in the coal mine". If those players spot an imbalance, that imbalance may eventually show itself on ladder. You just have to have games played so evenly that they routinely make it to the extreme late game before you notice.
Will the hives imbalance that the OP is claiming exists appear in ladder 2-5 years from now? Maybe... As players get better and games become more even... maybe exploitation of hives will eventually show itself as a significant balance issue in the ladder scene.
Of course its going to appear on turtle maps first, every game on those maps is focused on the late game.
NOTE: Again I'm not trying to take sides on whether Hives are actually OP, just trying to provide perspective.