This rule is just about giving you an additional right that you did not have before, namely staying in other Schengen countries than Italy. It doesn't restrict your right to be anywhere.
It doesn't even restrict your right to be in France for any amount of time, if you somehow qualify for it in another way (say being the spouse of an EU citizen residing in France). It just means that this Italian visa doesn't give you the right to be in France indefinitely.
Italy may have rules that invalidate your residence permit if you stay out of the country for too long. It might also be necessary to show that you haven't interrupted your studies and are making progress. I have no idea whether that's the case in Italy or what the specifics might be but that's completely unrelated to the 90/180 period and I am not aware of any European state using that particular threshold for this purpose.