Eh, time for another practical consideration. Yes, ofc a bunch of stuff was illogical, I'm not defending that game if you pay me.
But, err, did any of you guys play Fallout 1? You know, the one where the super mutants are in fact pretty much an uninteractive Orc/ogre horde sacrificing their captives to their eldricht abomination monster god thus making more of themselves?
Fallout 2 was pretty much a huge WTF Bizzaro retconing regarding that. Check the name of this site? See it? Why would a fan community, unless theyr'e batshit insane, call themselves that unless at some point Fallout 2 didn't exist? There was once a world where the idea of Ghouls as harmless put-upon trading card game playing goofs, or having a super mutant in your party would totaly and completely break immersion in the world of Fallout.
The game that brought us super mutants and ghouls as anything other than ogres and orcs respectively also brought us gems like talking deathclaws, fake vault 13's, the entirety of Monthy Pyton and the holy grail reenacted in disjointed episodes throughout the wasteland, the temple of trials with the self-repairing solid metal doors and handy plastic explosives in a jar, the whole concept of vaults not being genuine bomb shelters, many different reuputations for sex and depravity with only a token badge for becoming a ranger or a sherif, a quest which lets you cover an entire map with heaps of crap out of just one toilet, a shotgun wedding, a magic 8 ball, ghosts, gauss rifles, visions, color coded geckos some of which breath fire, 200 Hp chinamen who get the "gave up demoralized and leaderless after your rampage" endgame cutscene if you throw a plant spike at a random guard before entering a tanker, more miniguns than any sentient race ever had reaso to develop... and had close to no radiation or titular fallout. Or the Brotherhood of Steel. Or even it's own original main bad guys. It's also really, really all over the place in terms of setting, story, genre, writing, content, precedents, quality, balance, state of completedness upon publishing, continuity, sense, mood, consistency... It's hell'a fun though!
So to someone asking what were super mutants doing in Fallout 3, the answer, of course, is making sure nobody sayes it's not fallout because there aren't supermutants in it. Just like what they were doing in Fallout 2. It's a long standing tradition, ever since Fallout 2 was made to be more of a diesel punk - western - monkey island mashup with a lot of humorous references to the original Fallout. The ghouls and mutants in the two cities that house them (there's also 2 in NCR) were complete WTF moments as far as the Fallout universe up till then was concerned (far more improbable than the ones in Fallout 3), the ones in the Military Base had nothing to do with the Master except conviniently walking into where the vats were, and the ones roaming around the end zone of the map and right next to the capital of the NCR were there because - heck, we have no endgame, so mutants, otherwise this isn't fallout. The supermutants that you can fight in Fallout 2 really don't make any sense, as they would've been wiped off the map long ago.
Basicaly, they were there because the Military base is where it is on the map, and since they wanted vault 13 in (but didn't really know what to do with it either, so talking Deathclaws because, why not?). Shady sands, and Vault 15 have to be there since they're all on the same paralel. And so is the Military base, so why the hell not? Because it was thoroughly destroyed in the first game? And you have a ton of new stuff that the new hero could be fighting? Naaaah, instead of properly introducing the new bad guys a bit, let's just stick mutants down there and call it a day. Saves money since you can just reuse all the old models and stuff. Even better! Instead of putting the new bad guys there exploring the ruins, let's make it so that they turned into super mutants while they were at it, cuz, you know, supermutants! And let's even give them supermutant gear even though they would've had the new bad guys gear, cuz they weren't masters army? But then we'd have to make new animations for them! Well, they could've dropped them and found all this stuff, it was a mutant military base! But what happened to all the gauss rifles and new stuff they had before they were sealed there? Shus, that would totaly mess up the careful zone by zone linear gear/threat progression... (beat) ...which totaly isn't there, because we're selling it as non-linear seeing how we couldn't be arsed to come up with a coherent plot or coordinate people designing different cities, if we had all that we wouldn't need supermutants in the first place! And make sure that the player gets a ton of XP just for finding the place! But, dude, you can't miss it, there's nowhere to go but San Fran after NCR and this is like right in the way. Exactly! So give them a ton of XP and stick a Power Armor down there, the supermutants are easy to shoot - noone will complain that none of it makes sense. You know players, give them a shiny set of armor and a 2 AP per shot gun they'll think it's the best idea ever! But what do they need the power armor for, there's a stronger armor in a bloodly locker like, one quest away! And you know they'll go straight for that one because it's the only quest on the entry map and the only BoS quest in the entire game? Yeah, but theeeey don't know that! But still, dude, they've seen Supermutants before, I don't know... Ok, here's what we do - do everythign I've said, but stick a magician summoning a bunch of other monsters right at the bottom. Make him a supermutant, too. (Pause) And if anyone asks how he's doing it - he's tossig gebrils into the vats and deathclaws come out! So it's science and not magic! And make HIM drop a piece of the new gear, while you're at it! But just one. So the players still have something to loot off the main bad guy. Brilliant! Right, so, um, who's the actual bad guy this time around? The prezident of the United States! The same United States which have been blown to kingdom come way before the first game started, which is kind of the basic premise of the games entire universe? The very same! Brilliant! Ok, supermutants it is then, and a wizard who is a supermutant, the bad guy is the prezident of a country which hasn't existed for even longer than the supermutants have been defeated, we got that sorted out, and that saves us a few days and some cash, anyone got any ideas? Yeah, I got one, how about if we pay the guy who designed Modoc to make a new map of it which is exactly the same except covered in shit...
So - supermutants! I'd say Fallout 3 really screwed that up, the time before that it wasn't just brand recognition, it was also model recycling.
(I do love Broken Hills though, this is just me fooling around shareing a bit of perspective. Sorry if all the Fallout 2 references got a bit sidetracky, but it's an ancient thread and I just felt inspired).