I'm sure you are familiar with invisible walls that you've run into. These are called blocking volumes in the engine.
A lot of what you've described can be fixed by adding blocking volumes around meshes. The crossbeams above 7 are meshes. If blocking volumes were added which are the same size and shape as the cross beams ,then you'd no longer get stuck in them. Meshes use surface collision and blocking volumes use volume collision. Surface collision just isn't very good. Volume collision requires something called a 'closed manifold' to work and meshes aren't always the right shape to do that.
It's hard to make blocking volumes that match the mesh perfectly. Fixing the castle ruins in Dria using blocking volumes would be difficult. Any mismatch would result in invisible walls, so you trade one problem for another. The engine does have a feature where you can select a mesh and create a brush out of the mesh, then you can use that brush to create a blocking volume that matches, but it doesn't always work and is difficult to use correctly.
There is a lot of random crap (meshes) in Ganja's Room. I had to do a lot of work creating blocking volumes so you wouldn't randomly get flyers and mantas stuck everywhere, but it's still easy to get stuck on that map. It's a problem with meshes, but BSP maps (inside maps like DM style maps) don't have this problem.
It's a ton of work to go back and refine these old maps with better blocking volumes. Maybe if the pay were better