namely, the depleted fuel reprocessing recipes that take both acids. They can't be made using any vanilla structure.

Are they intended to be used with some of your other structures?

That's right. You can use the sulfuric acid recipe, you get the same result for the same amount of acid. The recipe that uses both sulfuric and hydrofluoric acid is only slightly more efficient in that making hydrofluoric turns 10 sulfuric acid into 20 hydrofluoric acid. But other than that they're the same recipe, so you can make everything in vanilla, but you can look to my chemical mod if you want more buildings with more input and output options. It also involves more chemicals, though, at an earlier stage of the game. So it adds more complication, specifically a few new puzzles...

Does that recipe only intended to show up if there's a machine with enough imputs?

I just made the recipe available regardless of whether you have a machine that can do it. I figured that way if someone else has another chemical plant from another mod that has more inputs, it will work with that, too. There isn't a native mechanism to turn off recipes the way you suggest, although I'll considering coding one into my factorio data library.