Mostly this feels weird when you have a structure from another mod in a thematically appropriate location where you really wouldn't expect regular zombies or skeletons to be spawned instead of husks/strays.

Is there a way to have husks and strays spawn as special variants of those mobs from spawners added by other mobs without them turning into other random zombies/skeletons instead?

I'm using Special Mobs 3.1.7 on MC 1.20.1 and Forge 47.3.11

very true, will have a look at this

Im pretty late to this, but I plan on adding a config option to disable random replacement from spawners, so that like you say, the only replacement that happens will be special counterpart instead of normal random replacement

Partially fixed; added config setting to skip processing of spawner mobs entirely