Doesn't matter, the points have been lost. Pecco was/is faster as evidenced by the Q2 session.
Unless Jorge make an epic mistake during Sunday's GP, it's likely a done deal. I mean, never say never, as one can't predict what the final race will be since there's so many variables, but I wouldn't be putting money on Pecco to retain the title right now, even as much as I want the factory team to retain the title.
I don't know if your software/setup argument holds-up though. They have access to each other's data, as do all of the GP24 teams (I don't know if the GP23 teams are excluded from that sharing). If there was a setup advantage, surely the factory Ducati team would know about it and use it as well.
I think MM has it next year though. On a year old bike he manages to finish 2nd in today's sprint. He's clearly not afraid of crashing and has a lot of race experience to draw on.
If Pecco had finished 6th in the 8 DNFs he's had (assuming an even split, 4/4, between GP and Sprint races) he'd be 29 points ahead as of right now.