So I plan to make a set of stronger-than-vanilla modules that will be included with my mod when I release it. However, when I looked at the images for the Vanilla modules, I noticed odd chunks of the image that are not the normal transparency pink color.

Could someone explain to me what those are there for?

The mat image has that portion of the sprite as background, so the foreground image there is not even looked at. You can color it any color you like.

well if that's the case, what is the pink bit needed for?

It's not, it's just there.

oh, alright. thanks for your help, duh.

Not a problem. As an addendum, bunker module backgrounds should be entirely colored unless you want the terrain to show through, and bunker module mats use the terrain palette, not the normal one.

i already knew that, but thanks for the information anyway.

The "pink bit" shows where the FG image will not cover. If, for example, there's a "pink bit" on the foreground where there's a valid color on the BG image, then you will automatically (so long as the MAT matches up) only see the background, with no FG.

The brown is just a compression artifact due to the slightly unusual RLE format Data uses for his bitmaps. Paint has problems displaying it, but saves it fine. It also sometimes causes problems on scene bitmaps, with big blue spots. If it bugs you, just floodfill it pink; it won't affect anything.