it depends ...
on the programmer. Programmers have different levels of skill and knowledge.
Sure the registry is well defined, but most of the details of the definition are not available to the general public. Since the registry depends on those "universal ID" "numeric code names", if you don't have access to the cross reference translating the ID back to specific applications, you (as a programmer) are probably going to be conservative about messing with it.
Also, every programmer does not have access to the details of how every program has done it's specific registry entries.
Also, there are differences in opinion on what constitutes a "bad" registry entry. Is it an "orphan" entry for a program that has been uninstalled (I think yes)? Is it a file extension "associated" to a program that is no longer installed (I think yes)? Just to name a couple of common 'errors'. There are many more to be considered.
The end result is that every "registry cleaner" program has a slightly different set of criteria it searches for and "corrects". You have to find the one(s) that agree the most with how you think (and that don't cause crashes with your specific installation details: OS, drivers, applications ...)
