Yeah, Sock's tutorial is certainly covering a lot of things that only apply to Quake 3 (or compatible engines).
I cannot claim to be an authoritative source regarding Quake editing - I'm not a veteran mapper and have yet to properly release a single (!) Quake map (apart from the betas in this thread). I try to adhere to following rules:
- Most vertices I only displace on one axis. So if I want to push the rock surface in, I'll grab a vertex and just push that one in exactly according to one axis. I try to make sure my brushes keep quite some volume (no strangely flimsy brushes), which is why I start with 128x128x128 cubes. I can push those around without
- I try to keep all vertices on-grid. I certainly make sure all vertices are on integer positions.
- be gentle on the floor, don't go as crazy on vertex editing as on rock faces. A few hills and ramps usually work fine, but if you go overboard you can run into collision issues, like players getting stuck on random edges (for Quake 2 and 3 the collision system works quite differently and seems to be overall more robust).
I uploaded an example map with sources over at https://maikmerten.de/base1/start-wip.zip
- perhaps that's useful for you. However, again, I might do things horribly wrong although they appear to be working fine for me for now ;-)