here is the quake speedrunning discord
If you want your times to be officially accepted by the community and want them posted on speedrun.com or similar you pretty much need to use neaquake or joequake. That is pretty much the standard.
Yes, the difference in protocols between the engines means you can get more speed. Watch some of the streams from beehivekay:
The tricks he does aren't possible in "normal" engines. He doesn't want to set times, he just does it for fun / practice.
So I guess it depends on what you want to get out of it.