Believe it or not, but I played through Fallout 1 about 4 times before I learned that the Master wasn't the super mutant lieutenant at the Mariposa Military Base. The game ends after leaving Mariposa a smoldering ruin, so that's where I always ended it. Didn't ever even SEE the master until my most recent replay through it this year. Also, yeah the master seemed to be part computer so it's possible that he uploaded himself before the bomb went off.
And reguarding Harold... According to a lot of posts I've seen, FOOL will take place before he gets rooted in place. I'm thinking that some of the unused but known story from Van Buren may play into the making of this game. In which case, Herbert is starting to take over, but still leaves Harold free to walk around. (Yeah, yeah, his name's Bob. I think it's funny
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So for both, there's the chance that they'll be alive from the game's perspective. Personally, I think that it's a no-brainer that Harold will be alive, but I think the graffiti about the master was just... graffiti.