Good question, and I'm happy to provide clarification.
1) DM rolls
First, I never said that I don't want you to roll something. What I'm doing, however, is preemptively roll for "passive" checks rather than asking you to do so. This eliminates a lot of back and forth in such situations, greatly speeding our pace, as follows:
Normal tabletop play
DM: You enter the corridor. Please roll for traps.
Player: I got a 22.
DM: There's a nasty blade ready to spring from the side!
Player: All right, I'm trying to disable it... 18.
DM: Success! Now you can open the door safely.
Accelerated PbP play
DM: You enter the corridor, as usual you're looking for traps. You get a 22, then you disable it with a 18. You enter the next room, etc.
Now, even as I do that, if you post a roll IC as you describe your next move, I'm going to use it, not duplicate it. Indeed, when CleverDragon rolled a 25 for Perception today, I took that result to determine the outcome. I rolled other things later, to determine what Vershab made of the tapestry, rather than asking him to roll.
2) Players who don't have the best bonuses
Well, if I rolled everybody's Perception every time the group entered a room, there would be 99% guaranteed success to notice traps. Same for Knowledge rolls. So I'm rolling only the best of everyone; or, in the case of Perception, I'm rolling for the character who's first in the marching order. There may be circumstances when rolling everybody's check is warranted - for example, if the group is ambushed, then those who succeed in Perception will not be surprised. When applicable, the team members with lower bonuses on something can use Aid Another to improve the success chances of whoever leads in a certain skill.
So, no, the skills of those who aren't the best at somewthing aren't being ignored.
Does that work? I'm totally prepared to take your feedback and make changes if something makes you uncomfortable.