Can I swap the inputs/outputs the vanilla factories?

Yes

Can I swap the inputs/outputs of this mod factory?

Yes, if the mod does add the recipe as a recipe it should create all the possible swaps. I didn't test on every mods available but Angel and Bobs seems to be fine.

I can't swap the inputs/outputs, why?

Look if you already have pipes connected. Because you can't swap if you're going to mix fluids, just remove the pipes and swap

When I swap this recipe the recipe itself changes, why?

It's because the mod create all the possible permutation of the recipe at the end of the loading, but if a mod modify a recipe after that, the changes won't apply to the permutations and lead to that issue. I'll look into it if this issue happen too much

My game is stuck on the loading of the mod, why?

It's probably because something went wrong this the mod. This shouldn't happen but in case it does report it with the mod list so I can fix it ASAP

My game crash with an error, what happened?

Probably an error on my side, report the error I'll fix it ASAP!

The swap system isn't really easy to use, are you gonna change it?

I'm working on a GUI so you can select the recipe you actually want instead of cycling through all the possibilities.