Good to hear it's not just me dealing with these issues. And to be honest, four setups on the lighter side for me. There are many parts we make where I have 7-10 setups at times. The library then becomes a nightmare. especially if you don't rename your operations like I did in the above example... trying to remember what "contour4" was or "drill2" is just isn't feasible.
I normally name my setup folders that program number, so the posted file, setupsheet I make, and the setup folder in fusion all have the same "5555" or what ever. I then rename each operation using that 5555 and adding .1, .2, .3, etc. That way in the tool library, within all that mess, I can at least see which setup and which operation that tool is for. Not ideal at all, would also be nice if that process of renaming could be automated. Like setting a rule with a name and an auto-sequencing number at the end.