Idea Summary
After upgrading your theme, all region and item template options are lost. You expect to maintain all those options when initial template has the same options as the final template. If you select completely different templates it would be fine to reset all template options but not otherwise.
Current behaviour makes it really difficult to updgrade themes and this leads to an eventual use of deprecated templates. After upgrading theme you must review the whole application to fix all visual template options that may have been lost.
Use Case
Use a template, define some special options, for instance, define a region without borders under template options. Upgrade application theme, all your template options are lost, and region has borders again.
Preferred Solution (Optional)
When swithing or upgrading a theme, APEX asks for the matching between intial and final template. In case both templates have the same template options, those user settings should be kept.