Unless something is putting on a bunch of "portable apps" that are basically just unzipped to new folders I don't think it's a good idea to do mass changes at once to your system. The more variables, the less chance of figuring out what went wrong.
I don't even use auto updaters unless they are for one program only.
When everything is a jumble you get stuck using a restore point or image restore and that's a pita usually.
A slip-streamed disc install utility is another matter. But in that case you often have to test it for days to get the script right.