Right now, seems that if your mod loads before other mods that change recipes for fluids, your permutations will stay with the original ingredients and only the main recipe will be changed.

Not sure if this happens with every case but I noticed this in SeaBlock with MoreScience and all his extensions.
The basic fluid 2 has the recipe changed to not include inserters but if I permute the recipe, it shows the old recipe with the old ingredients.

Factorio really needs some kind of tag to indicate that the mod should be one of the latest one to be processed....... This would prevent having to add lots of optional dependencies.

This is how Factorio works. It already has the equivalent of such a tag - data-final-fixes. But when multiple mods use data-final-fixes they cannot all be the last one, so this happens.

I am reluctant to add optional dependencies to all mods at this time. Maybe to the bigger ones.
Factorio 0.17 introduces the hidden optional dependency. When that comes out I will feel better about adding more dependencies.

While not ideal, as a workaround before 0.17, I suggest manually adjusting the dependencies - something quite common when creating a custom set of mods.

And as a side note, I am not going to go through all mods in order to consider whether to add them as dependencies. If someone (or a group of people) lists such mods somewhere (like here) it will make the process easier (and faster). However I want links to the mod (if extensions are applicable - links to them as well).

0.17 came out.
I have added more dependencies.
Let me know of other mods that have to be added.

Hi there, this mod would be ideal to have this qol added: https://mods.factorio.com/mod/Thaumaturgic-Machinations