I have the same vault on my pc and phone via syncthing, I’d like different themes as some don’t look great on mobile (or get laggy).
I’ve tried disabling sync with the .obsidian folder on both devices but that’s just disabling themes on startup. It’ll begin loading with the last selected theme then switch to default halfway.
I’m a rookie here, just a few months in, but I have my vaults syncing via Resilio sync. So, similar to your setup I think.
I have my data folder on level down from the main vault level to separate the data from the .obsidian folder. So the .obsidian folder doesn’t sync. Because that whole level doesn’t sync, any app settings don’t sync. Annoying and a blessing.
I do have a sub folder at the bottom of my actual data folders zzzObSettings and in there I will copy a copy of my .obsidian folder in a 231219-FromWork folder and then when I’ve made enough changes, use that to overwrite my at home machines.
I’m working on using this to keep my instances the same, but I would think this system of selective syncing will also work to keep things different. The only catch is, you miss out on all your other settings like book marks and such. They are all hiding in your .obsidian folder somewhere.