Each user profile on your Switch has one save file for Sword/Shield. There is no separate save file for the expansion pass (which is a DLC purchase and not a separate title on the Switch in itself) - the benefits of the pass are applied to your one save file as soon as you reach the Wild Area for the first time.
Save files are stored on the Switch itself, not the game card, so it doesn't matter which game card you have inserted unless it is of the other version.
Additionally, if you have set your Switch as your primary console, all profiles have the benefits of the expansion pass as well.
If you want to have a non-expansion pass save file, you can create a new user profile on your Switch, and a new save file on that profile. From there, you can simply ignore the DLC passes and never go to their respective areas.
Otherwise, your save files are the same because they are the same singular save file.
If I'm misunderstanding the situation, feel free to correct me and I'll edit my answer accordingly.
