I didn't even notice the lieutenant the first 2-3 times I played fallout.
"Gizmo, the Khan's leader, the Master, the Deathclaw in the cave at The Hub, The Maltese Falcon guy, etc. They're all bosses. Also, the lieutinant isn't optional, there's no way to beat the game so that he lives."
Gizmo is ONE fight. How that constitutes a boss of a level is beyond me. The deathclaw is one fight out of potentially two fights with deathclaws. Again, it is a big stretch to say there is a level at all, let alone boss of a level. The maltese falcon guy, again, is one fight. He has no level. he is a guy. Same with hightower if you kill him. The khan is not some uber fighter bigger and tougher than all the other raiders combined, either - I suppose he comes closest of your examples, but he is not only irelevant to the game but he is not in the least uber or contrived or unrealistic. Hitler in castle wolfenstein is a perfect example of a boss monster.
All your examples are fucking ridiculous.
"There's a few side scrollers where the boss pops in, does something that you have to undo or bipass, and then they pop out." That's called a cutscene. Then you usually fight him at the end of the level or else at a later level or the end of the game, or whatever.
"That's not true. Hell, even Diablo 2 had bosses which were optional. Blood Raven, for example, you can completely ignore and finish the whole game. Blood Raven is definitely a boss monster, completely optional, and we're talking about Diablo 2 for shit's sake! Even action CRPGs have optional bosses, so why question the ones in Fallout? " I didn't play diablo, but the basic paradigm of a boss is to have a boss at the end of a level, and not one of your examples matches this.
You don't blaze your way to gizmo through 200 thugs and then see gizmo has dual miniguns and some weird superpower.
There are people who you can fight, but not contrived idiocies like that in the game.