With all due respect, it seems that once you get an idea in your mind (often at least partially correct, to be fair) you tend to harden it and sometimes exaggerate it beyond recognition.
The Jazz's five man lineup with Donovan, Ingles, Bojan, Royce and Rudy was the third best 5-man lineup in the NBA last year out of lineups playing over 30 games together (+12.9/100 possessions). Replacing Ingles with Conley made it the 6th best lineup (+9.5). A difference, to be sure, but the latter was hardly "clunky."
And while it's true that Conley and Ingles overall didn't have a super 2-man lineup rating (+2.2) over the whole season, Quin did eventually manage to find a lineup that worked wonderfully with them together (with the bench crew of Clarkson, Niang, and Bradley: +16.4 -- too bad this lineup appeared only in 13 games?)
I'd also argue, in any case, that this type of data isn't all that stable, especially from year to year. Last year, you're right that Ingles and Gobert worked great together, but the previous year, the Ingles-Gobert combo was in the lower half of the Jazz's 2-man combos that included Gobert (very close to the Exum-Gobert combo, in fact). That year, Ingles was much better with Favors, which is likely where he'll spend a lot of time this season.
I don't mean to argue that Quin, by virtue of his experience and expertise will necessarily end up with the optimal lineup choices (though I will trust him more with that than anyone here, myself included), but I think that arguing from the past only gets us so far, especially if we're overlooking the fluidity of these types of things from year to year (or perhaps even month to month).
