For some reason when I start a new game on Nauvis the crash sequence is missing after installing this mod. On other planets it works. Even when I uninstall mod, crash sequence is not showing up.

EDIT: It might be problem caused by other mod. Will check it deeper.

EDIT2: Yep, it is conflict with some mods that give you stuff at the startup. This mod works properly, so probably some startup script infighting ;)

Removing the mod after starting a world won't make the crash site appear after the fact, it only spawns in on new worlds.
I guess I disabled the crash site on Nauvis no matter what the setting is in order to spawn it on the other planets, and I figured it didn't matter because why would anyone use this mod to start on Nauvis? I can change it when I get home though, because I guess someone could accidentally have the mod enabled on the Nauvis setting when trying to start a new world and it would be a lot more annoying to have to remake the whole world instead of just disabling the mod.

Edit: I guess I did handle Nauvis correctly according to your edit. Mind sharing the mod that was causing the problem so I can maybe try to fix it?

https://mods.factorio.com/mod/red-quickstart

What is interesting, that mod only messes crash sequence on Nauvis, other planets are ok, so it is probably some Nauvis surface event conflict.

Interesting, I know the mod author so I'll see what I can do, I'm not at home right now but I'll take a look when I get back.

I talked with the mod author and his mod is supposed to skip cutscenes (it is called Quickstart after all) but it was actually a bug that it wasn't skipping the cutscenes from the other planets. They fixed it on their end, so now it actually skips all cutscenes. Thanks for the report on an otherwise very hard thing to catch!