No "elegant" way of doing it, maybe, but that doesn't mean there's no way of doing it. The traditional solution is to actually set MF_Boss and MF2_Fret on the enemy and take it off when invincibility was supposed to end - but manually doing stuff with Fret was only really necessary because we couldn't anticipate taking damage, otherwise we'd have let the boss thinker manage that part for us. With the damage hook though you can guarantee it gets put on before damage is applied though, so you might be able to stick MF_Boss on with that to get flashing and take it off later without having to deal with fret at all.
That was good enough to get you the normal color #000000 flashing, but the whole-sprite flashing brak has might be restricted to certain mobj slots. If I were trying to do this back in the day, I might have resorted to replacing the crawla commander or something if I really wanted the silhouette flash.