So there was a thing I noticed about a month ago, and it's that you can kind of leave the playable area of the map by just bumping into the skybox brushes/solids. I initially thought it was a bug I probably caused at some point, but I later compared it to another map I made months ago and it was all fine. I then switched to Vluzacn's HL Compilers (I actually have been using them since my first CS map, but only because I needed to embed a custom .WAD file), re-compiled the map and it got fixed. I never bothered exploring it again because for now VZHLT does the job all fine (even if the compiling process takes a bit longer to complete).
Now, using a test map, I compiled the same version using different compilers: the ones that come up with Half-Life SDK (on Steam) and Vluzacn's compilers, and the skybox solids are indeed semi-solid. You can go through them and even fall into the underground deeper than intended, but there's a point where you just get stuck.
If either the .RMF or .BSP is needed, here's the link to a folder containing both: https://drive.google.com/open?id=1eqa95JeciYwklcXTOLxavBzjubZMDWy9
The map was compiled using the "Expert" mode, although no additional parameters were used.
As a sidenote, this would perhaps explain that one collision bug on cs_assault where you can get inside a traincar.