How important is it to have a light color on top and a dark on bottom for radiated heat?
This is offered at the risk of Richard Nisley coming back with an answer based on measurements (which always trumps amateur theorizing).
Fabric darkness is unimportant from a nighttime warmth point of view. Radiant heat transfer can be large but only if there is a reasonable temperature difference between the yourself and the liner fabric or the shell and surrounding objects. That will only happen if there is significant conductive heat transfer happening (too little insulation) … in that case you will already be cold while failing to sleep.
However, a dark color can be a good thing when drying the quilt/bag in the sun.
However, I also feel obliged to point out that one of your premises is faulty. The "darkness" that your eye sees results from how the fabric reflects visible light. Radiant heat transfer happens via infrared (longer) wavelengths. Choosing material for more or less radiant heat transfer requires knowing the material's thermal emissivity. The archtypical example is snow which reflects visible light like crazy but emits (and absorbs) infrared very very well.
For over stuffing, does it make the quilt warmer or does it just make sure there aren't cold spots?
I believe it helps in both ways. Richard has posted some info about warmth vs density of down fill and it makes a noticeable difference. Unfortunately, that one has not (yet) made it into my collection of useful Nisley bookmarks.