Looking at screens of the Amiga port leads me to think that the Amiga has a larger color palette but can not put as many colors on screen at once(maybe 50 or so).... i know nothing Amiga.
Yup. It has 4096 colors for the master palette, but normally is only
32colors onscreen for sprites and BG to share (64 colors for half bright for the BG - afaik it doesn't effect sprites and you wouldn't want it to, but it's not really that colors many because the half bright process will yield redundant colors. In other words, it doesn't create more colors through half brightness than what's already in the master palette). They use also are known to use hsync effects (copper) to change the palette for the BG on certain scanlines. It has it's limitations though. Games developed around the Amiga's limitations can look really impressive/nice. Ports sometimes suffer because they can't always take advantage of said trick with such results. If you look at Bonk on Amiga (BC Kid), the screen shots have a good color count - but that's because they are changing the very far background colors as it goes down the screen. The tiles and overall BG themselves (and along with some sprites) actually have less colors than the PCE port. And as you know, the PCE is very minimal looking. Same is true for PCE Parasol Stars port to Amiga. Lower color count, missing colors - but they don't do the vertical gradient effect (it also doesn't scroll like the PCE one between sub levels).
As a test, I color reduced and rescaled one of the arcade shots to compare it with the PCE version. They look really close, except the dev team/artist took extra time to workout the palette choices (instead of my automated conversion). Looks like they did some manual dither/touch up too on the PCE pics. They did a great job converting them over.
Left: Arcade(PCE converted). Right: PCE