@DannyM, I'm not familiar with messengeruser.org but from what I saw when I looked there, it looks to me as though you'll continue to sign into Skype with that same exact Microsoft account.
The chat program that you sign into will change from Messenger to Skype, but you should still be able to sign into all Microsoft services using your existing account, if I am understanding correctly.
I can see the convenience of moving synths or panos from one account to another with comments, favorites, etc. preserved, but it isn't a necessity.
If you look at other free online services (flickr, smugmug, vimeo, YouTube, etc.), transferring ownership of uploaded content from one account to another isn't something that they generally offer either, so I'm not too surprised that Photosynth doesn't.