In all probability, yes.
You can remove Pep from the equation, but that doesn't mean you also remove City's squad (under another hypothetical manager) from it.
Sure, it's conceivable that United might have limped over the line as PL winners that season if you remove Pep (and replace him with a pretty shite manager) - yes. But it still wouldn't have had the appearance of Jose's last title winning season with Chelsea. Because that season they looked genuinely solid up to a certain point - after which they, sort of, hung in there and dragged themselves over the line in a decidedly non-glorious fashion. But they actually looked solid for months. We never looked solid at any point, by contrast. We looked shaky as feck - a disjointed team capable of moments of brilliance and carried in several, crucial matches by a goal keeper making statistically unlikely saves time and again. If we had won the league that season, it would have gone down in history as a very shabby title campaign - clearly worse than Chelsea's.
ETA It is also very easy to make a mockery of the idea that points total - or even league position - is an accurate measure of how good a given team actually was. You - obviously - have to factor in
more.
Sacchi's AC Milan vintage won the Serie A in 1988. They then secured their reputation as one of the greatest club teams ever by winning the European Cup in style - and then defending it the following season.
But that team did
not win the league in any of the seasons when they triumphed in the European Cup. They came 3rd in '89 and 2nd in '90. Had that happened today, I have no doubt a certain category would have been all over it, pushing the idea that this historically great team - with Baresi, Maldini, Gullit, Van Basten and Rijkaard - were a bit "overrated" (quite possibly "frauds" to boot).
Of course, a bit of context helps here: the Serie A was insane in those years, with Inter's "German" vintage (who won it in '89) and Maradona's Napoli (who won it in '90). But that's pretty much the point - context. You don't judge a team by looking at statistics in isolation - unless you're a feckin' idiot, that is.