Leroux: It's not the concept per se that is annoying, it's just bad implementation of the concept. Personally, I like the idea if it makes the finale exciting, challenging and fun. But it's a thin line between that and totally frustrating. And what from my experience often makes it frustrating is when such boss battles drag on for too long, meaning you'd have to invest a lot of time when retrying and doing a lot of things over again.
It's no fun to die for one small mistake after struggling to stay alive and slowly diminishing the HP of a boss for more 5-10 minutes or so. It's no fun if you can hardly harm a boss and there is no other trick but to slowly chip away at his HPs for all eternity. It's no fun if you have to fight more than three forms of a boss without saving when each battle in itself is epic already and you first have to learn how to defeat him, at high risk of life, like: barely survive first fight, get killed while learning how to manage second fight, repeat first fight, get killed in second again, repeat first fight, barely survive second fight, get killed while learning how to manage third fight, repeat first fight, repeat second fight, get killed in third fight etc. etc. This might work in some cases, but it becomes extremely repetitive and frustrating quickly, if the battles are not fun or drag on for too long.
I have a few games that I nearly played through and mostly enjoyed all the way but then abandoned because of the frustrating difficulty curve in the finale, and IMO that should not be the goal of a developer, to make the finale extra frustrating. It should be challenging, but still enough fun to make players want to try again instead of making them rage-quit.
I was going to write something similar, but then bumped into this and that pretty much explains my viewpoint. The very thing you describe on your last paragraph happened to me in Torchlight while playing the mage class. I pretty much saw the ending on Youtube, went "THAT'S IT!?!?" and never finished it. Also, I don't know how I managed to beat the meat circus back before they softened up the Psychonauts finale, but I really, really wanted to watch the end movie, which was the only reason I kept trying, though I felt thoroughly frustrated all the way through!