Misery, are you keyboard and mouse or game pad normally? And do you tend to walk during most boss battles?
I use a PS4 controller for this. And I do tend to use the slowdown button alot.... but I'll also sprint whenever it seems conceivably possible because I have no patience. Like the hard-mode version of the Warden's 4th pattern? That tornado that spins in two directions at once? Yep, gonna sprint through it. Takes too long otherwise. Might not seem like the best move, but I dont really get hit by that. In normal congested patterns though it really is best to use the slowdown.
The padlock idea sounds cool, but it'd give me the wrong impression - I'd start looking for something to break, or otherwise get distracted when I should be dodging bullets. The simplest indication I can think of is have the boss' health drain on its own, which would immediately tell me that oh, this segment is timed and I need to wait it out.
That's one to put on Mantis; Chris or Keith would have to deal with that. Definitely outside my realm of design. I cant do the engine stuff; I just make the game try to destroy you, heh.