My mistake, I tested more and found out that Discovery Tree isn't related at all, I can reproduce the bug with only this mod enabled.
It's not that recursion technologies can't be disabled but rather than the map setting will only persist when set at game creation, if changed afterwards there's no effect in the tech tree.
This one and QRD fork have this same behavior.
The original Factorissimo doesn't exhibit this problem, changing the setting during runtime results in the expected change to the tech tree.