Wow, I didn't realize that the PCE & MD Hellfires were so different. I thought that they were both fairly straight ports from the arcade. I prefer different versions for each shot. I don't remember how much extra variety, animation, etc the PCE version has, but if I were to judge them
strictly by these screens and taking into account that (I believe) the MD version has some parallax and the PCE doesn't, I'd say that the MD version looks better overall.
SD2 does have some AWFUL boss flicker
Really? I never experienced this. I only got the game recently and made the equivalent of two runs through each on real hardware and Magic Engine. It really stood out to me how little flicker there was considering the size of the bosses and when it was obvious they were sprites and not tiles. Even a boss like this didn't flicker for me-
Of course, I don't view flicker/break up as an unacceptable or bad thing, only when it affects the gameplay. If the price for getting a screen filling boss is the occasional thin horizontal stripe cutting out or appearing transparent for a fraction of a second, it's fine with me and I'd gladly take that over a flicker-free SNES game with tiny sprites to avoid slowdown.
The only other explanation I can think of is that maybe I just happened to play some flicker-light routes on real hardware and the game has unadvertised SuperGrafx support like Super Darius 1 that automatically kicked in on Magic Engine.