In addition, we have no universally accepted definition of [what is part] of the operating system.
We could rephrase it thus:
- "What kinds of modules should be included in an operating system? What kind of a module should be considered part of an operating system?
- "We don't know! There is no universally accepted definition of what is part of the typical operating system (and what is not part of the typical operating system)."
Imagine you have a list of 1000 modules: I/O drivers, text editors, graphics procedures etc. And someone asks you:
A great collection! But which are part of the operating system?
In your example, the word what is used instead of which because the number of components that could be included in an operating system is well nigh limitless nowadays.
Regarding your idea:
What I think this is trying to say is probably that there is no agreed-upon definition of what does the term "part of the operation" system mean. If that's the case, then why not say it like this: In addition, we have no universally accepted definition of what part of the operating system is.
Had we wanted to say this, we would've added the indefinite article a, because "part" in this sense is a singular count noun:
We have no universally accepted definition of what is a part of the operating system.
Compare:
We have no universally accepted definition of what a planet is. (or " [...] of what is a planet")
(Kudos to Stephie for her comment on the implied clause "What is not part of the OS".)