Unfortunately, I was hit by what I assume is a bug, as shortly after Mariposa I got the Vault 13 game over cutscene well before the 500 days (less than a year had passed).
About the "less than 500 days"-bug, I have never seen that happening and you are pretty much the first to report this. There is nothing I can think of right now that would trigger this, unless you used the CoC doctors unusually frequently (using them reduces the invasion timer by 1 day)... or you simply traveld randomly on the worldmap for 500 days. If there was no time skip, the invasion can't trigger.
There's at least 2 in-game ways to shorten the timer to the V13 invasion: asking the water merchants to ship water to vault, and through specific dialogue choices with (either, I can't remember) the talking-head Mutant guarding the water pump in Necropolis or your discussion with Lieu in Mariposa.
Did you do either of those Gilius?
Holy crap, I didn't know that. Looking it up on Per's guide, I see:
In v1.0 buying water from the Water Merchants shortened the other time limit (the mutant threat) by 90 days if it was currently at 100 days or more, but this isn't a factor any more.
So, is it a factor in Et Tu? I know the config file lets you disable the 500 days timer (or set another), but I didn't find anything in particular about the Water Merchants affecting the timer. I did disable it in my game afterwards, but I don't think it works with saves. Besides, my invasion date was slightly before a year had passed, so even with extra 90 days it doesn't add up to 500.
And no, I didn't give up the Vault's location to the Lieutenant (I've made several playthroughs after, so I'm not 100% sure anymore, but I believe I would've mentioned it). You can overhear the conversation where he discloses finding about Vault 13 (you can sneak up to him, get 1000 xp and leave), which is what I usually do. Regarding the mutant in the Watershed in Necropolis, what happens is that if you fail the speech check he'll offer to take you to "Lou" (or else fight) , and the game simulates trekking all the way to Mariposa, which deducts some 40 days, or similar. I don't think there's anything in particular you can reveal about Vault 13 to the dim-witted mutant. And no, I didn't follow that route.
In any case, the mutant invasion occurred AFTER Mariposa turned to dust. I think that can also occur in the original, but you got to admit it doesn't make much sense.
I've forgotten lots of things about quests, which lead to some frustration at times, as the patches still haven't fixed everything. I wasn't able to complete LA's gang feud peacefully because I didn't speak to people in the right order, for example.
I don't think I remembered things correctly, here. I had imagined you could solve things peacefully, but no, the Regulators or Blades must die, with or without you taking part in the battle(if you side with the Blades). The one weird thing is that if you tell the Blades' leader that you're gonna talk to Zimmerman (this is right before the attack, after solving the Gun Runners quest), she subsequently disappears when you return to the map. If you don't have the holodisk (which I didn't, because I hadn't talked to Zimmerman before), you can't even tell him about his son's death, so your only option is to initiate combat with the Regs yourself.
The most unenjoyable part of the game for me are still the random encounters. I don't disable them because travelling the wastes should be dangerous, but being ambushed by 10 mutants with rocket launchers is not very fun, particularly when you have 10 Luck and +80 Outdoorsman. Even when they're not particularly dangerous, they become annoying very quickly.
Pro-tip about random encounters: Study the random encounters map to avoid mutants as much as possible:
https://fallout.fandom.com/wiki/Fallout_random_encounters
I've slightly changed my opinion on random encounters, as they can add some excitement to an ironman game, which is how I'm playing now. Mutants are a Russian roulette, but the others you can manage. It forces you to plan ahead. I'm still not sure how much Sequence and Perception really help.