While playing the vanilla game with custom settings like friendly accuracy i encountered the bug that dont matter how much you set bases to capture, enemy faction (or very rare your faction) will have only two bases.
Encountered only while play with two factions.

Which map is this in?

Mainly on Black Gold Estuary. Very rare appear on Moorland Trenches.

All right, got it. Some maps use designated starting bases, which may overrule the player made choice for number of bases to capture.

Some of these maps have been setup with all bases distributed between a specific number of factions, like it is with Black Gold Estuary.

Some maps, like Keepsake Bay, only require certain bases to be used as designated bases for different factions, the rest of them in the center area are distributed according to the number of bases to capture.

Given how Black Gold Estuary has been made, the fix would be to hide the number of bases to capture option there. Thanks!

Moorland Trenches on the other hand should not have this sort of issue, all bases are freely distributed between any number of factions. With some quick testing, it seems to work as expected there.

Oh. Well. Alright then. Thanks.