PUPs are NOT 'pretty much rootkits,' they are what it says on the tin, Potentially Unwanted Programs. Rootkits really aren't programs that are unwanted as they generally aren't installed by the user, but there are programs that use rootkit style functionality to protect themselves, etc...
Many tool which can be used for good or evil fall into that category as if installed by the user not a problem (it is serving its good purpose), if it wasn't installed by the user then it is more likely to be unwanted.
Switching on PUPs during scans, does require an amount of knowledge of what is on your system and why it might be considered a PUP as you will have to make an informed decision when avast alerts should it find one.