It seems pretty clear that Permanent Affinity was the plan from the beginning. The game started chopping boxes off right from Episode 1; something was going to have to happen once you ran out of CHICK/DIK boxes. Whether it works well in practice is another matter, but it was clearly not some last minute patch to fix a failing system. My guess is it will work much like the Affinity system as a whole: good enough to convey the general idea, but not able to stand up to scrutiny. We'll just have to wait and hope for the best.
That said, implementing it halfway through the game makes sense to me. If you wait until near the end of the game to introduce a big change, you don't have much time to explore the consequences of that change. If the Affinity system is meant to illustrate how our choices shape the MC's path to adulthood, then having lots of time to see how our choices pan out is a good thing.
After all, just because the MC isn't sleeping with, say, Sage doesn't mean we must skip new content with Sage entirely. We can still get platonic Sage content - potentially even unique platonic Sage content. Yes, that increases DPC's workload, but it would make the game a lot more interesting if he pulls it off (and frankly, I don't think we can stop DPC from increasing his own workload at this point). Again, we just have to wait and hope.
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