Will there be any problems if the tomboy in 2 OS are of different version?
It depends on if the structure of the config files is materially different. In the case of TomBoy, I suspect that it would work ok since that file is basically a data store anyway. I am guessing however. I don't have two versions of TomBoy to compare data stores. I would suggest you try it and see. You shouldn't hurt anything and you can always delete the symlink and rename the original config file back as it was.
I cant create one user in first OS then I cant import that user in the other OS
If you use different usernames for the installs you will have permission problems. Well... not problems, but you will have to change your permissions so all the users have access to the same data. If you use the same username, you won't have to address this issue at all.
I thought the UUID will only change when the partition are moved / modified.
This is correct, but you have to think about all the ways a partition is touched. When you install you format at least the / partition. This changes the UUID. If you have an existing install that has that partition mounted then it will be confused by the UUID change. Also, if you resize a partition or move it up against another partition, it will sometimes change not only the moved partition's UUID but also the adjacent partition you moved it up against. UUIDs are very fragile in general. Almost any action that touches the partition will cause the UUID to change. That of course causes problems with any existing installs that use UUIDs as unique identifiers.
I hope that helps clarify things for you.