How does this handle being placed from blueprints?
If you pick up a permutated factory, does it give you a different item, or just the original one?

How does this handle being placed from blueprints?

It works with blueprints - whatever the permutation of a recipe was when you created the blueprint, the same permutation will be set when you place the blueprint. (Just a note: the blueprint will not be vanilla - it will require the mod).

If you pick up a permutated factory, does it give you a different item, or just the original one?

It gives you the original one. This mod works only with recipes - when you change the permutation, a different recipe is set.

How do you deal with building on the blueprint if it's permutated

The permutation is just a different recipe. So there is no special interaction with blueprints.
You place the blueprint, the ghost will have the correct recipe set, by the game itself. If a bot builds it (or you place the building exactly on the ghost, with the correct rotation/facing/direction, the correct recipe will be set. This is the vanilla mechanic.

So you could potentially have a slew of permutated items in your inventory?
There's recipes for all this in your build menu too?

There is no such thing as "permutated items".
The recipes for permutations are hidden.

So the blueprint pastes down a permutated entity that you cannot craft?

No.
There is no such thing as "permutated entity".
This mod only adds recipes.

The new recipes use the same items. He changed only the order of ingredient / products in these recipes. Thats why u can change the input / output of a building. No new entites or items - only new hidden recipes.

A permutated factory would be a new entity because you cannot alter Fluid boxes of an existing entity.

I'm asking because I have a similar mod design with my pipes and when you bp a rotated pipe you can't build that one because the recipe is hidden. Then it turns into bot networks cannot place that building.

I figured this was why you were asking so specifically :)
Especially considering your mod. Looks cool, but I haven't had time to try it yet.

But this mod does not do much with entities. It does not add new entities. The only thing it has to do with entities is to get the entity you are hovering over in order to "rotate" its recipe. So it will not be any help for your case.

I am guessing you could do what you want (in your mod) with either the "on_player_setup_blueprint" or "on_player_configured_blueprint" events - maybe you can change (in the blueprint) the "rotated pipe you can't build" to something that you can build. And https://mods.factorio.com/mod/blueprint-train comes to mind as doing something of that sort, maybe take a look at that. And then discord is always an option.

Sorry I cannot help you more at this time.

I mean I could easily change it to place a ghost of the buildable one.
I assume yours is only changing the filters for each fluid box then?

It changes only the recipe with a different recipe where the order of the fluid ingredients and/or results is different (permuted).

It does not manipulate the filters of the fluid box in any way.

The mod does only one thing related to fluid boxes - when the recipe is changed (via scripts) while the entity is crafting, the fluid boxes are emptied and so some fluid is lost. I take a note of what fluids were present before I set the recipe and then insert the same amounts of the fluids in the appropriate fluid box.

So, the fluid box filters are being shuffled around then?

No. I do no shuffling.

So, the input recipe dictates the order of the ports?

Yes - the order of the fluids.

Oh. Didn't know that did that. Nice!