But this is why it doesn't work. The MC can think and act like DIK while having CHICK affinity because it's the status choices that have more determination on this than the affinity choices. A CHICK affinity MC can do everything they can with Quinn, be friends with M&J, and have DIK status, yet because of that one affinity check, which could be based on making as little as 2 more CHICK than DIK choices, his offer to help is rejected. In this scenario, Quinn's decision still does not make sense because the status means he acts more like a DIK which is what you might say she likes, but she'll reject him because of this other system that overrides that.
Also, if there are only 3 direct actions with Quinn required for that scene on the DIK path, then you could say that she doesn't require much to gain her trust and since affinity seems like less of a determining factor of personality and behaviour than status, it again seems questionable as to why this puts her off. I honestly don't think there's any logical reason, storywise, to explain this, and it's just an arbitrary way to force content on to other paths to make the game more replayable even when this content separation so often doesn't make sense within the narrative.
But there aren't 3 direct actions to get Quinn's scene, there are 4: you need DIK affinity (however you get there). You seem to be using the fact that it requires an Affinity check as proof that the Affinity system doesn't mean anything because there are other checks too. That's circular reasoning. Each decision can have its own consequences, but the Affinity system is intended to represent to net result of all those choices on the MC. I agree it fails at that task, but I disagree that a better system wouldn't serve a useful purpose.
You say a Neutral MC can do all the things a DIK one would and so Quinn has no reason to reject him, but that just isn't true. In the Neutral case, DIK actions by the MC are a bare majority at best. In the DIK case, they are a solid majority at worst. If there was a clear logic to what constituted a DIK or CHICK decision, that distinction would matter. Sure, a Neutral MC might be willing to take advantage of Quinn, but would he really have her back when the chips are down? Based on his actions, it's reasonable for Quinn to conclude he might not (again, assuming the Affinity system made sense).
Of course this is why I think the Permanent Affinity idea is a bad one: when the system is this arbitrary, what's the difference between restricting the choice and denying it was a major choice to begin with? Yes, neutral characters can potentially combine choices in a way that Locked characters can't, but is that really any different than keying non-choices off specific actions? If the only way to make get a choice in Episode 10 is to go back in time and reverse a different choice in Episode 2, does that really make the character feel different in a coherent way, or is it just upping the opportunity cost to respec? I say the latter. DPC is letting his hatred for min-maxing blind him to the shortcomings of the system he designed.
But again, we're stuck with this version of Affinity so we might as well make peace with it and hope the rest of the game is worth it. That's a separate argument from whether it ever makes sense to have NPCs react on their own based on things the MC has done previously (rather than giving the player individual control over each outcome). IMHO denying the player direct control can help if it establishes the NPCs as independent actors with their own thoughts and feelings. Like any tool, it isn't inherently worthless just because one guy used it incorrectly, but it may only be useful on projects that just don't interest a given player.
All that said, I think the idea this is being done for play balance reasons is just plain wrong. If the goal was purely to balance content on different playthroughs, there would be no need for all these extra checks. Unless you think DPC plans to add unique content specifically for Neutral/CHICK MCs that accepted Quinn's offer, had sex with her on the roof, and rejected M&J, clearly something else is at work here.