I think that it is because Dier was picked over Alderweireld at the beginning of the restart and bought straight back into the side after his ban.
I agree with you that Alderweireld did enough during Dier's absence to make him first choice but I don't think that Dier was as bad as you are making out before that. I worry that they are too slow to play together regularly.
For what it's worth, see links below to Dier's positioning vs Sheff Utd and his corner marking vs Palace. I think the Sheffield Utd goals are clearly more forgivable, and I'm not saying he's been horrific overall, but I don't think he's been great. (Appreciate these are just three one-off instances, but they're from a small sample of games, and obviously for a centre back each and every mistake can be very costly. Also appreciate that others were at least as at fault as him for the Sheff Utd goals!)
To be fair sounds like you and I aren't too far apart in our assessment. It's more those who see Dier as being the #1 CB and/or part of a very small group of title-winning starters that I find weird.