If the reason to leave the ending off the MS-Dos version was the limits of disk space on floppies, how did the Amiga version include the ending? Did Amiga have a better file system?

The MS DOS version was released first. Amiga was a later release, and got upgraded with the ending.

Fun fact:
The Amiga version came on floppies, 2 i think it was, at up to 800 KB per floppy.

The GoG install is just over 100 MB...Doesn't look or sound better than Amiga, if anything Amiga sound is better.

So how'd they end up with ( at least) 50 times the size on PC...

Original PC release was 3 HD Floppies, so aprox. 4,2MB.
GOG probably adds the Emulator and other stuff (manuals, etc.) which take up the rest.
But yes, it still is crazy :-)

I found the Amiga version of Darkmoon on an abandonware site. What difference, if any is there between the two versions?

Concerning EOB2: Amiga has only 32 colors. DOS has 256 Colors VGA graphics.
The game content is identical.