Based off Microsoft's help descriptor of the FontTextureProcessor class:
Monochrome characters should use white for solid areas and black for transparent areas. To include multicolored characters, add an alpha channel to the bitmap and use that to control which parts of the character are solid.
Since you're editing the font as a BMP bitmap, it's not going to have a separate alpha channel. This is the reason that black or dark areas are being treated as transparent.
You'll need to edit it with software that supports an alpha channel such as GIMP or Photoshop, then export it to a PNG (with transparency enabled), TIFF, or any other such format with alpha support.
So let's take your original image:
So let's open it up in GIMP. The first thing is we need to separate the layers, the white has to go. To do this we need to select the "Fuzzy Select Tool":
Under the "Tools options" on the left, I would recommend setting the threshold to something around 100-150 for best results.
Now select the magneta background, and use CTRL+X to cut it. This should give us a white background with the letters still intact. Now we need to create a new layer:
Use CTRL+V to paste the magenta area into the new layer. Now use the Fuzzy Select Tool again to select the white areas, and delete them. I had to first right-click the layer on the right-hand side and choose "Add Alpha Channel" for this to work correctly.
Now in GIMP it should look similar to this:
Now we need to go to File -> Export. Select the PNG type, and you should have a dialog that looks somewhat like this:
Those options I have selected should give the best results.
Now we get the result with proper alpha:
Note: I intentionally left out the white areas within the letters. That is left up as an exercise to the reader.