Ah... yeah, the code assumes the origin for cylinders is in the center, so having it be in the top left corner will offset everything by the radius amount on both axes. Glad that got sorted out in the end at least.
The player movement (the vast majority of movement is done in psbp_inertia_horizontal / psbp_inertia_vertical) mainly uses two functions, terrain_hit_pilloid_cheap and slope_hit_optimized, the latter of which in turn uses terrain_buffer_lookup_verticalslice. Both of these intentionally just check 3 points (XY center @ Z bottom, Z top, and Z centerpoint) since collision checking turned out to be the most expensive operation in the game. But there's a dummied-out alternate version of terrain_hit_pilloid_cheap that does check the full 12 points (taking the radius into account). Replacing the 3-point version with this, and then using slope_hit_pilloid_cheap in the player inertia functions instead of slope_hit_optimized, should restore the old collision checking as it was. (Note that slope_hit_optimized uses a z height argument that slope_hit_pilloid_cheap doesn't use so you might need to remove that to avoid GM complaining about passing too many arguments)