So to fix the problem we abuse the way that the fontself decides how to place a glyph vertically. Since it picks a median point, the trick is to make the bottom of a character you want to be lower (like a comma) to have less non-alpha data on the bottom of the glyph than the median characters have.
Eagle eyed readers will notice the font is a bit different, we're porting the fix over to the original font now.
The numbers have a lot of glow around them. The glow forces the tool to detect the bottom, effectively raising the bottom of the character. The comma, without the extra glow can be visually lowered.

With a little finagling the overall effect works out pretty well.

If the glow isn't viable/desired for the font I suspect that adding a single pixel vertical bar at the bottom of the glyph would have a similar behavior, but that hasn't been tested.