I think DMs are going to do it regardless, whether they want to or not.Are you saying that if the DM wants to use particular obstacles and the PC, via their build choices, imply that they don't, the DM should just roll over and do what the players want? Because that's what it sounds like.
If a DM ordinarily likes have chasms and pit traps in their dungeons for challenges, but every single PC in the group can fly... then that essentially eliminates chasms and pit traps as possible challenges (unless the DM comes up with scenarios where flying doesn't work.)
Now on occasion I think the DM WILL decide to put in the occasional chasm and formulate it in such a way that the party won't all be able to use their flying to get past it... but those will be one-off scenarios in the story. Other than that one occasional time... chasms and pit traps are otherwise off the table and the DM knows it. So they just won't bother with them. Not because they are rolling over to player choice, but just because there's no point in including them since they aren't actually an obstacle any more.