The deviations from standard have been catching up recently. I haven't thought about it, but looking back, this is represented in most of the few super8 commits in 2015. -sndspeed and entity alpha come to mind.
I've fussed occasionally about map/mod deviations which should not be supported. Engines should avoid bad-behavior, which is anything that is hard to code for software-mode

A nightmare example that emerged from Rubicon Rumble Pack is entity alphatest (fence texturing). Really should only be set per-texture with texture flags. Texture flags in Quake means naming conventions. We might could use a simple shader system. starting to get off-topic...
Test build with cl_beams_quakepositionhack cvar: