Unless for some reason the space liquids do not count as intermediaries
the entire lineup of the decontaminationfacility (making space water, chemical gel, etc...) do not work.
Neither does the recycling of scrap.

The production of delivery cannon capsules doesnt either.

Switching "all" back on does make it possible but that makes little sense.
By every possible metric i can think of "Space water" is an intermediary.
But its SE, who knows what nonsense got programmed into that.

I believe SE counts these as finished products to prevent duping (I have no idea why they need to do this, productivity is already banned in space)

With the cleaning, cooling etc i fully understand.
Whatever. By now i changed so many recipes to make them bearable might aswell continue on.

I've recently discovered that SE is restricting where you can put Productivity Modules, not even allowing them in Assembler Machines and Electric Furnaces, the 2 places they're needed which makes no sense. I was hopping this mod would allow me to put them in those machines again, cause apparently the author of SE really hates productivity modules, but it doesn't.

It should work correctly. Please try enabling the "Allow for all recipes" setting. If it still doesn't work, tell me the recipe you are trying to use modules with. (I assume the machines have slots for the modules and they just don't work - if there are no slots, this mod doesn't change it)

all recipes, any item, simply put, I can't put productivity modules in anything while SE is active, though turning off SE and mods reliant on it, and it goes back to normal. I can only put in speed and efficiency modules while SE is active, though it doesn't seem to care about the god module mod that combines them. I also got a mod that lets me put Productivity modules in beacons, tho they don't affect the machines I can't put them in anyways.

I think the beacon mod might be messing with this mod. If you link it, I'll add a dependency so it loads correctly. (If you can, please also include the mods you have so I can check if anything else is breaking it, you can find it at C:\Users\<User>\AppData\Roaming\Factorio\mods\mod-list.json)

is there a way to get the list to you, these message boxes have a character limit and copy and pasting it is waaaay to much, and trying to copy paste just the names would take a long ass time, I have 232 mods installed atm.

Ok, I went around disabling and enabling mods, deleting redundant mods and gradually working my way up till all non offending mods were enabled and still allowed productivity modules. The offender I found is Krastorio 2

Edit: okay, so, it's the Combination of Krastorio 2 and Space Exploration, either on their own is fine, but together they disable productivity modules, I went full bare minimum with all other mods aside from their required mods and this mod disabled and figured this out. So, with both K2 and SE enabled, Productivity modules can't be used, but with only 1 or the other enabled, I can use them.

Pushed a fix, now K + SE works. The problem was there because this mod loaded before them, and they canceled the changes after that.