I have some questions on the colors.
The "transparent black parts" all seem to be RGB = 0,0,17.
The "non-transparent black parts" all seem to be RGB = 1,1,1.
How did you convert these colors?
It's been a while since I did the conversion so I don't remember for sure. But I believe the bitmaps in the game were all 8-bit indexed, meaning each pixel is one of 256 colors selected from a fixed palette. So the 0,0,17 and 1,1,1 comes from whatever the palette says. I believe in the bitmap the transparent pixel would have value 0 (ie. palette entry #0, which I guess apparently has color (0,0,17)).
Likewise the "non-transparent black" is some other entry in the palette. Actually, now I think of it, it is possible that the palette may originally have the RGB as (0,0,0) for non-transparent black, and my conversion program purposely make it (1,1,1) instead to make it easier on other programs that may consume these bitmaps treating (0,0,0) as transparent.
I do think that if you run the actual Mac game, they really do use RGB (0,0,17) to paint the background (in other words, the background is not exactly (0,0,0) pure black like on the PC version, but rather this shade of very dark blue as the RGB value suggests). So in that aspect the (0,0,17) is accurate as well.
I should be able to modify my conversion program to output in other ways. For example, I can make the bitmaps be 32-bit ARGB and just encode the transparent/non-transparent information as alpha.