The mentioned programs can change the file volume levels so that all MP3 decoders use the changed volume level. AFAIK, they adjust a scale value inside each frame in the MP3 file. The process is practically lossless, because it does not change the encoded data anyhow. Only the resulting output volume is adjusted. This kind of scale adjustment is not known to cause any audible problems, like audibly decraded S/N ratio.
Foobar uses the same (or at least very similar) software code as MP3Gain, but it has less available options.
I think the command line MP3Gain program could be called by a plugin if someone would like to investigate the possibility to create one. Perhaps also the JRiver developers would be interested in finding out if that kind of feature could be integrated in MC. The MP3Gain source code is freely available. For example, a feature to automatically volume level synched MP3 files during the sync (with any portable) would be a nice add to MC13's feature list.
For now, it is quite possible to adjust the files after "syncing" with an external program.
Personally, I first sync a virtual handheld on a local hard drive with MC12 so that I can adjust the synced files before using them with multiple devices. After adjusting the files I use MJ12 for syncing a couple of small flash memory devices and burning MP3 CDs for my car. I have set MJ12 to monitor only the virtual handheld location so its library is small and fast to use.