Fill the channel with black silicone, set the window in, let it cure, trim with a razor blade.
Keep it simple!
I use Permatex Ultra-black gasket maker. I guess some people call it silicone. I don't no if it is, but I do know that it holds door glass very well.
It is still possible to remove the glass and sealant should you break the glass in the future.
Great solution - thanks!
I've also used black RTV to mount window channels and side window fuzzy wipes; in both cases it held perfectly.