A bit late to the party, but glad you heard from the Good Dr. himself and got some clarification.
As far as primary sources go, the SGZ is as good as it gets. Each of the three kingdoms had an imperial historical office whose job was to produce records of what happened in the kingdom. When Jin absorbed Shu and Wu, those documents (some of them not quite done) got shipped over to the north as well. Chen Shou was the closest person we know who had access to all the original primary sources (since the originals have not survived). He put together the accounts as best as he could, sometimes having to pick and choose from conflicting accounts (think about the "fake news" phenomenon we're dealing with today--if it's *this hard* for people now, who have access to a great number of instant sources, to figure out what's true and what's not, how much harder would it be back in Chen Shou's time?).
Later compilations of history, such as the ZZTJ, drew largely from the SGZ.
Pei's notes are supposed to be *supplemental* to the original text and must be considered in the con...text of the SGZ text. Some of his notes are for clarifying Chen Shou's text, or pointing out places where there was internal inconsistency (or just inserting his personal opinion...). Other notes are meant to provide additional information or perspective (some sources are obviously more legit than others; back in his day he'd assume that his readers would be able to tell which ones were the equivalent of the National Enquirer).
Obviously, just as with all historical records, it's necessary to understand the context of the work (for example, Chen Shou was obliged to elevate Wei over the other kingdoms because of the political situation he was in), and understand what the sources of errors, omissions, and intentional mistakes could be (incomplete primary materials, the whole civil war thing, him being too close still to the time of the events to have a full perspective, etc.).
If you can read Chinese, you might want to look for Chinese books/research articles citing or discussing the SGZ as a historical source.
(Glad you didn't end up comparing the SGZ and SGYY--it's done before and it's a huge project. I have a copy of the SGYY with side-by-side text comparing with the SGZ accounts, and it's huge, but it's not even complete. )
PS: I find it strange that your prof would say that the SGZ/commentaries are "highly fictional" rather than "inaccurate". Very different terms with very different implications. You may want to force some clarification out from him.
PPS: You will also want a definition of "historical source", and make sure your thesis addresses exactly that. I mean, you can kind of argue that it's not a *primary source*, since it's been processed and compiled by Chen Shou. Also, "fiction" has an element of intentionality--you have to be actively making stuff up (or be heavily deluded) for your work to be considered fiction. I have read biographies where I know the events or situations weren't quite as they're described in the book, but I wouldn't call those fictions--I would call them "accounts of history by some very confused/egotistical/narrow-minded/inexperienced people". If the SGZ was written to be a historical record, it is a historical record.
The SGZ is also unlike the other official Histories in the Chinese canon, because it only consists of biographies. Could this be a source for your professor's claim?
I wonder if your professor could be thinking about the Jinshu
instead. It is more like a traditional history, compiled by a team of historians and containing both biographies and timelines and records of cultural things, but it a) contains some pretty outlandish magicky things (see my translation of the Jinshu's biography of the monk Fotudeng
), b) has an obsession with gossipy things that really belong to a tabloid magazine, c) contains lots of inconsistencies, particularly with dates, and d) there was an intention for the work to be a Lesson to the Tang court (effect much amplified in the ZZTJ--I mean, look at the title of that book).
But since your prof had raised that question, you really should get a definition from him and work with that. Always always answer the question.