Jasper, the creator of that noclip site you mentioned near the end, made a comment on your video regarding the feasibility of your idea. It might be best if you responded directly to them in the YouTube comments section, but here's a copy of said comment for prosperity's sake:
Quotetl;dr: You want Garry's Mod.
Hi there, I'm the creator of noclip.website, so I'd say I know quite a bit about the internals of different games. Let's get this straight out of the way: from a technical perspective, this idea is nearly impossible. Compelling, of course, but the magic behind games is a lot more tricky, nuanced, and special-cased than I think you imagine.
To use your "take Train Simulator and add zombies" example: I haven't played Train Simulator, but from the footage I've seen, the train's on rails. Do you think that game even bothered with collision data, or AI pathing data for the zombies to run on? What would the zombies even do? All the zombies I can think of in games are encountered in close hallways to ambush the player; so they move slowly, their AI is designed to trap you, and when they get close, they stand in one spot and hit heavy. Spawning a few in Train Simulator, well, someone has to animate and program them being shoved out of the way when hit by a train. To spawn in a zombie from Half-Life 2 and just expect it to "just work" is setting up a scary expectation for games and for developers. I'd say we're pretty good at our jobs, but not that good.
Not to mention that this workload only goes up as we add more elements. If we add, say, Octoroks in, now we have to plan for three "pairs" of interactions: Zombie/Train, Zombie/Octorok, Train/Octorok. With 4 elements, that's 6 pairs. So, in a way, adding "just one more thing" is the hardest part; and most times this happens, developers don't plan on supporting all interactions. In your software, where the player can do literally anything with any game, you are committed to implementing all of that.
I think a lot of early game developers start out with "I will make a game where you can do anything" as an idea (I was that way once as well!), but quickly learn that the constraints in the game's design are what make it fun. The elegance of Portal was everything they didn't add, it meant it was possible to keep the entire game in your head.
Garry's Mod is probably the closest we'll ever get to your dream software, and it's great! I love Garry's Mod, but it's still very limited in its scope compared to what you want, despite having probably the biggest scope of any of these tools. And it still doesn't come with fun out of the box, you have to add it in! Thankfully, there's a huge community doing that, and so you can play Prop Hunt in Peach's Castle from Super Mario 64 if you want to.
Don't get me wrong, some of these levels and worlds feel so real, feel so close, and I totally understand how compelling it is to feel transported to somewhere, and want to stay longer. That's why I originally built noclip.website, after all! So I understand your passion here, I just want you to know what you're asking for here, lol.