...it really boils down to if they think their coach can make [a QB] excel with their skill set.
Kind of.
I think GMs are hoping to find someone who can (1) transcend being a "system" player and (2) possesses the physical ability for potential Playoff success.
To that point, I would think GMs across the NFL would largely favor Herbert for his availability and scheme-transcendent physical attributes. There's more upside in that given that both Herbert and Tua have similar career numbers in many categories like Y/A, TD%, INT%, etc.
You pointed out how McDaniel is the "perfect solution" for Tua which pretty much defines him as a system-specific player. When Tua was put in a lackluster situation, his efficiency declined and his production was generally awful. Put in similar circumstances, Herbert's production remained a bit better, adding credence to the idea that his floor is higher.
It was when Tua was put in the ideal situation that we saw him produce with an efficiency that Herbert has yet to reach. This was the whole argument for drafting Tua over Herbert >> that there was ultimately more upside in Tua (which I think '22 and '23 have shown is there in some form).
So it's really a question for the GM as to whether he wants to deal with the headache of trying to build the perfect "Tua-style" offense and I would wager that most GMs wouldn't want that problem knowing that the Tua offense has performed so badly in clutch moments and has yet to carry it's team to any sort of Playoff success. The "upside" hasn't really proven to have much "up" in it.
You add in the injuries and physical limitation that Tua has and I would wager GMs would take the easier choice of Herbert almost every time.
FWIW, I don't love Herbert. I think he lacks top-tier efficiency but I would assume most GMs probably see far less headache in working around a more conventional QB like Herbert who's floor is higher, stays healthy more often, can put together some gawdy numbers and who requires less specialized treatment.
Remember, Tua was the preferred prospect back during a time when many looked at Justin Herbert as Ryan Tannehill 2.0. Now that Herbert has proven to be far more than that, it's understandable that his stock is actually probably a bit higher than Tua, particularly when Tua has been given 2 great chances in '22 and '23 and yet nothing's come of it.