I've done some testing and found that the original 500 day deadline (400 days if you have the Water Merchants deliver to your vault) is restored in the Restoration Mod. In my opinion, the Restoration Mod helps give Fallout the polished feel that it lacks. Now if you enter a city after the deadline, people are no longer standing around alive and well as if nothing happened, which was odd.
And as for Necropolis, if I want to get the good ending, I'll have to postpone killing the mutants at the watershed before tackling the Cathedral and the Military Base.
Yes, I did kill the master first. I went back to Necropolis after to tell Set about the Master's death, only to find that the city had already been invaded by the mutants. I guess 30 days had long passed since I killed the mutants at the Watershed.
I forgot to mention that in my recent successful playthrough, even though I never returned to Necropolis after killing the mutants and fixing the pump, when I got the Brotherhood to help assault the outer military base, in speaking to the elders, I had the option to tell them that the mutants had already invaded Necropolis, even though I never went back there or even heard about from anyone else (such as Patrick).
The mutant timer is the one thing I don't like about Fallout 1 as it forces you to basically speed through the game to get the best ending. Since I am the type of player who level grinds deathclaws in Adytum, does all the quest, reads enough skill books to get 91% in First Aid, Science, Repair, and Outdoorsmanship, and gets all the implants (except Endurance if my current value is even), I modify the number of days in the vault13.gam file and I highly recommend anyone who gets the Restoration Mod do the same thing. This way, you'll have plenty of time to get the implants, do all the quests, level grind in Adytum, read books, get Hardened Power Armor and the Plasma Rifle upgrade in Adytum, etc. I also think that you can change the deadline for when the mutants invade Vault 13.
If you're still interested, patch 1.3.6 can be found and downloaded here:
Fallout 1: Unofficial Patch 1.3.6. - Моды и Патчи - Nuclear City (nuclear-city.com)