That is displaying over VGA (and another reason for not wanting to hook up the Elgato)!
I think it's down to memory. That's the largest map in the game. It looked great on the build of nuQuake from the start of this thread (but crashed upon completion), froze during loading on the version of 1.2 with clipping resolved, and it displays like that in the newest release. I've not made any changes to the map between tests.
Start.bsp looked fine, as did any other map that I jumped to from there via the console, though mipmaps still appear to be missing (they looked great in the build found at the top of this thread).
The game also crashed when using noclip on ATFE1M1.
I'm not currently near my computer, but you should encounter this issue with the version of the game that you already have.
And my query on your sound engine was down to the number of issues I'm getting there, which I believe was always the case with Bero's port; some sounds pitched up, some sounds looping, random pops and fizzes when no sounds are playing, etc. Whereas the sound in Makaqu, and I think RADQuake (from memory), are as expected. Not sure if a transplant would be easier than fixes?!