and it's also unrelated to the E1L1 window clip.
In E2L4 (Fusion Station) it is possible to crouch into the area shown in the screenshot below, which is supposed to be impossible to get into.
The idea is that either the player shoots the switch, or finds the entrance to the secret area leading to it, but in r8494 one can simply walk straight through the tunnel.

This indicates that crouching is too permissive at the moment and may allow the player to pass through areas that are supposed to be impassable.
The cause for this appears to be revision r7488: "More player clipping fixes"