Hi @greyguru. I meant to comment on your previous question but I genuinely forgot. What I would suggest is the possibility of using the option to not export the parts of the theme you do not want to use. For example if you create one theme with all options included, this might be used on Site A (including ads), then for site B (not including ads) click the option to not export the part/section of the theme. This way you can have one overall theme but output only the required parts for each site. I know “Don’t Export” wasn’t intended for this but I think it could work quite well.
The one issue I see with this is that each time you export you will overwrite the last export which would mean you would have to back up the export of Site A to losing a copy of it when exporting Site B. I don’t think that’s to much of a hassle and once you make it part of your process I think it could work quite well.
