Yes, I figured this out too. I discovered this awesome counter move Niobe can do against Seraph, so I played the level over and over playing with awesome moves.
In case you are wondering, it was a move similar to the fight between Ballard and Seraph where Ballard catches Seraph's leg and attempts to punch him, which is caught by Seraph. Ballard then flips off Seraph's chest, kind of like a wall jump off a person.
Anyway, after I died unintentionally, I went online to research this interesting little progress thing, and I stumbled a across a sort of interview thing with David Perry, lead developer of the game, who talked about its development. I read it through and was fascinated by much of it. I came to this point where it talked about how the Wachowski brothers insisted that if you loose to Seraph you skip a whole portion of the game. Being a bad developing strategy, Shiny wasn't thrilled, but they did it anyway.
The interview didn't mention any other point - I can't image one anyway. I already tried loosing and winning to Trinity as Ghost, but the other bosses? Can't be. Just my thoughts. Quite an interesting aspect of the game, huh?
-DM31