The prosthetic route, yeah. But I don't neccessarily think it needs to be a full-on hours in the make-up chair glued-to-the face thing. I think it would be possible to simply make the cowl out of a very soft, stretchy, fleshy type rubber that will simply move with the actor's face. Something like what those funny novelty stretch balls are made from - it really would behave like a second skin:
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You might need to have a slightly more conservative brow sculpt, yes, which would suit me fine personally. Something akin to the brows on the Spawn mask, or perhaps the fear toxin batman in Begins. You could still have pretty much a very similar sculpt to the Begins/TDK cowl though. Such a material would allow a full-head-and-neck cowl to have more movement too, possibly negating the need for any head-neck separation.
Whenever I see Batman's mask move with his face in the comics or cartoon, this is exactly the type of material I imagine it is. It would even stretch with the actor's jaw opening and closing - rather than the actor's face be constrained by the mask. AND he'd be able to shove his head through the mouth-hole and push the top part back like a hood, as he does in the comics.
And of course, you'd have it be reinforced with rigid forms where it needs to not wobble - ears, nose, whathaveyou, and of course "in-movie" the thing would be reinforced for protection too - perhaps even being impact-hardening for that the brows are protected.