I reproduced the area where I got stuck in my testmap and tried a few things:
1) I made the area bigger and tried if I got through now: it worked. I thought maybe I could simply expand all affected areas to work around the problem, but I also got stuck again near the exit of that room. That would result it a lot of unnecessary patchwork, since lots of places in HQS are meant to be claustrophobic.
2) So I tried to go for the root of the problem. I recompiled map hq3_3 with the old Zoner HL Tools - and it worked. The hullsize of the player seemed to be just a tiny bit smaller and I could get through the tight areas even with wiggle room.
3) I thought that I could probably just use the old compiling tools for all of HQS to revert to the old lighting, so I don't have to fix those aesthetic differences. But - honestly, the new tools also optimize a lot and open up a few possibilities for later on. So to fix it, I tried to simply alter the player's hullsize manually. The hlcsg compiler allows a -hullfile flag, thankfully, and I remember Vino did the same thing for the black cube player in an early version of Halfquake Sunrise. I successfully minimized the hullsize of the player to what felt the same as with the old compiler tools - and now it works again!
(And here I thought my player model probably just got fatter over the years... :D)
I've recompiled all of Sunrise and started to replay all maps again.
Then I found new issues, similar to the ones of the cube version of HQS: Getting stuck after a loading screen, weird stuttering when moving along a slope, ...
Maybe I'll just use the old compile tools xD VHLT is probably a good idea if you start mapping with these tools in mind, not so much for upgrading existing maps.
Out with the new, in with the old :D