I feel that this is a map issue, rather than with Knuckles.
Yeah, so do I, there have to be some solid parts. But sphere pointed out on Discord that this is due to Knuckles buggy climbing code. Hm.
added Movement/physics label
This is because the highlighted red linedef is being discovered as a possible latch candidate, and it's one-sided since the removal of thok barriers. One sided linedefs are instantly considered climbable unless they are marked ML_NOCLIMB.
This can be fixed in the level itself, but I feel the code could get a little smarter about it.
The map way it can be fixed is by placing a sky barrier sector on the wall specified. This wad places one on the opposite side as well to make things look nicer and address it on the other side too if it was there at all.