That is just it. Before I've seen that productivity modules have been disabled but now you can insert them, which is incredibly overpowered.

Do you have "Enable Productivity" enabled? If not, you won't be able to insert Productivity Modules into Alchemical Furnaces once they actually start crafting items, and productivity modules already in them should be ignored. The restrictions are on the recipes, not the building. With that said, though - there's no harm in ALSO placing this restriction on the building, to avoid confusion.

Obviously, if you have "Enable Productivity" enabled, then you'll be able to use Productivity in all of the Alchemistry recipes.

edit Fixed... Well, let's say "improved" in 1.3.3. The Alchemical Furnace will no longer accept Productivity Modules if you disable Productivity in Alchemistry recipes. Keep in mind that if you have mods which enable Productivity (like Unlimited Productivity), those will override my settings, and that's intentional. It's why I moved recipe generation from final-fixes to updates.

Nope, and well at least for me they aren't ignored when I put them beforehand, even though when I take them out I cannot place them back in because they aren't allowed. Great, thank you

Yeah, changing the Alchemical Furnace's prototype doesn't retroactively remove effects already on existing structures. In fact, I noticed it linger for a tick in the Editor with time frozen. Not sure what to tell you about the effects not being properly blocked. They were on my side when I disabled the Unlimited Productivity mod and my own "Enable Productivity" setting. Check the Reconstruction/Generation recipes. Those should also refuse Productivity effects.