Okay, A different opinion.
DO NOT USE INVISIBLE THREAD FOR BABY QUILTS! Yes, I put that in caps to emphasize how important this is. Invisible thread, if it comes loose or breaks with use, can be a risk to a baby. If they ingest any of it, it can cut their insides. If there is a loop on the quilt where some has come loose and other ends are still attached, or a long end is loose and played with, a toe or finger can get caught and circulation cut off.
I would not worry much about different colors on the backing... with custom machine quilting, there are often different colors showing... and it can be lovely. Use the colors you want to use in each area, and use cotton thread.
JMHO
PS. You didn't ask about batting, but don't use poly batting in baby quilts. In a fire, it melts and causes terrible burns. Quilters Dream makes a fire resistant batting called Dream Angel that is wonderful for baby quilts. Or use wool batting. Again, JMHO