I think the directory is hardcoded into the packages inside the site.packages folder when installing Python wheels. So as long as the directory stays the same one might be able to get away with zipping it up and uncompressing it again at the target.
Or it might be possible to turn EigenCommander and EigenBrowser and finally EigenD itself into Python wheels, then a pip install EigenD would install EigenD to any desired folder.
Are EigenBrowser and EigenCommander pure Python or is there still some C++ involved?
And — isn‘t the main entry into EigenD also in Python, so it could be considered as a Python application with native extensions? In that case py2app or py2exe might be an idea to get a portable installation that feels like a usual standalone app: py2app - Create standalone Mac OS X applications with Python — py2app 0.24 documentation
Alternative to py2app: https://www.pyinstaller.org/