How one could override files in nested portal_skins folder?
The default behavior seems to be that you need to copy whole folder structures if you want to override a single file. This is a maintenance nightmare.
E.g. how to override file:
Producs.TinyMCE/skins/tinymce/plugins/table/js/table.js
... without needing to create a duplicate for the whole Products.TinyMCE skins codebase?
You cannot override parts of a nested skins folder structure. If you want to customize things, best to create a new tinymce plugin (like mytables) and copy only the files for that plugin.
Use z3c.jbot, and put a file in your jbot template directory called Products.TinyMCE.skins.tinymce.plugins.table.js.table.js