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well, it's not really the location of the folder that's the problem.
the problem as you are probably aware by now is how all the other modules and even the core of XOOPS itself, *gets* the files from the uploads folder & then delivers it to the users browser.
most frequent methods used in XOOPS are to use a url method to point to the particular file whether it's an image file or software download.
it's these methods that would need to be altered as you have mentioned, the url needs to be replaced with an absolute path. it's not so hard to do, but there are many many places and edits needed to the core and other modules etc that may have to be slightly changed to make that happen.
to make it global initially, it would probably be easier to define a global absolute path, either in mainfile.php or by an editable xoopsconfig option in XOOPS preferences.
the editable method would be preferred.
then you would need to edit each script that has references to the uploads folder and change that to utilise the new path.
if done via xoopsconfig, it would be a matter of $xoopsConfig['uploads_path'] in replacement to the url and/or path used by the script. altho i make it sound really simple, it will be a lot of work to do globally for every module and area that fetches files from the uploads folder.. as most methods would use a relative path defined from XOOPS_ROOT_PATH etc, these would need to be replaced with an absolute path.