I don't think this would be too difficult for JRiver to add. They would only need to add an option to read the Album Gain library field instead of the Track Gain field. If some files do not have an Album Gain value MC should fall back to Track Gain when these files are transferred.
Also, I don't think the existence of physical file tags matters (or at least it should not matter). As far as I know, these are not used when the iPod database is created because it is quite possible that the source files do not contain all needed info in the file tags.