These are in regular Novenka as well. I think it's just secrets for the sake of secrets, no lore but what the player makes.

The teleporter should be in the back of the secret base located inside the back hill in the desert section of the map or atleast that's where it is in normal gm_novenka

You can get to all of these places without noclip. for example. inside of the bunker behind a "wall" (that you can walk through) there's a teleporter that brings you to the core.

gordom freemen monument (aka gman)