I can only answer from the Ubuntu side, since I have no experience with OSX.
I'd recommend to have separate $HOME folders for both operating systems. So, while your idea will definitely work, you should probably name your users differently, so that the configuration files for the installed programs are separated. Otherwise some programs, which are available on both, Ubuntu and OSX, yet in different versions, might get confused if one is editing the configuration of the other. In order to avoid permission issues, I would try to make sure that your user has the same UID on both systems, so that effectively both home folders belong to the same user. In order to keep everything tidy, you can then symlink the relevant subfolders in one of the home folders to the corresponding folders in the other one (e.g. that /home/linuxuser/Documents is a symlink to /home/osxuser/Documents or the other way round).