If you know they are PUPs and you still allow them, then they aren't unwanted, the crucial word in Potentially Unwanted Program.
There are many instances of programs that do things that some malware may do, like system tools getting information on your system, etc. For an AV, etc. trying to determine intent is the hardest thing, e.g. did you install it for a specific purpose or was it installed without your knowledge.
As for your comment "Auslogics defrag places many PUP's on the system." it isn't placing PUPs on your system it is placing tools to do the job. The fact that MBAM is very fussy about what determines a pup, may differ from mine or Avasts, it is all about intent and that is what a user has to determine.
The PUP scan on some shields is off by default and for many people this is just fine as crucially they wouldn't have knowledge of what the program does exactly to answer any interactive question raised by an AV alert.
Some security based software have a very different idea of what PUP encompasses