Ne_Ruins was fixed back then in beta 14 of pre-v1.0:

http://quakeone.com/proquake/interims/mark_v_20150428_windows.zip

As you can see, that was back in 2015. The problem back then was "incorrect handling of entities with alpha=0" according to Baker. If he did anything in the meantime that undid this, it's clear why the crashes occur (again).

I am not sure if I had reported the impulse12 issue as well, but when I played Ne_Ruins with that beta build back then, I know I had zero crashes. 

"Mark V - Version 1.99 - Revision 2 (Stable?)
#2092 posted by Baker on 2018/05/08 23:25:05"

Have just tried "Revision 2" from post #2092

Same issue, same occasion.

Game crashes 

You will probably need to go back further. It's possible it broke last year or even earlier again... I never checked it a second time after the fix since I assumed it would not break twice. Makes me wonder which of my reported issues are still solved. Gulp. 

So I have tried builds dating back to 1001 (Nov 21, 2016) and it still crashes. This needs investigation.

Please download this savegame for testing purposes (zipped, 66 KB) and copy it into your ne_ruins directory, then load it with F9 ingame.

How to reproduce the issue:
- Go around the corner
- Kill ONLY the Death Knights
- Let the succubus with wings alive and let it resurrect the Death Knights
- Stay in FOV of the succubus, crash will occur eventually

Sad that this problem returns to the stable builds. However, couldn't reproduce the impulse12 crash. I can go back and forth through my weapon inventory without issues. 

I have just checked it out following your instructions.
The crash occured immediatly right after the succubus started resurrecting those guys. Yeah, that's pretty inconvenient to have this stuff emerging in stable builds.

Concerning "impulse12" related crash. You gotta have super shotgun and quad super shotgun in your possession.
Try to scroll previous/last/next weapon with any button you assigned to execute that action. The game freezes then. 

1) When I press "load game" then load the savegame and then press ESC button it shows me "load game" menu instead of Main Menu of Quake. That's a bit inconvinient because I usually accidentally press "Enter" button and load a save game while forgetting to save the game after updating my game progress thus it results in loading an old savegame :D
Is there an option to disable this kind of a "Remember last menu" feature ?

2) If you run across a nailgun ammo box while firing the nailgun - it stops firing for a half a second. Really strange. Same applies for Supernailgun. 

I think the impulse12 in Ne_ruins would need to be fixed within the mod. It wasn't made with impulse12 support and since that quad shotgun is an extra weapon, it causes problems. I believe s.o. actually made a patch for that, but I could be wrong. The succubus resurrection crash is definitely to blame on Mark V, though.

I also cannot run Ne_Ruins without assigning more memory to it via -heapsize 512000. Otherwise I get a crash right after leaving the intro map (Hunk_Alloc). 

At the introdution map of Quake, if you don't move your mouse and you go forward (move forward command) the player starts to look down at ladder a bit and if you go back (move back command) to the top the player centers his view back. If you move your mouse at the beginning - this behavior disappears.

Strange stuff, I think there must be a console command to disable such a behavior, but I can't find one.