I have never used Apple fitness so I don't really follow exactly what this issue is here. I don't know if it is one of those things where you can use a different Apple ID for fitness than one you are using for something else, or even if that's what you mean. As far as I remember seeing, iCloud is the only thing where if you are bundling you can use a different Apple ID for iCloud storage.
Put simply, Apple equates one ID as being one person. If you both use a single ID, Apple will see you jointly as being the same person and won't let you split things up unless an app provides that as part of something an individual may wish to split up. If you use differnet IDs, Apple sees you as being two people even if are one person with two accounts. It doesn't really matter if these are bundled subscriptions or what, it is all a matter of Apple IDs.
Apple ID Frequently Asked Questions - https://appleid.apple.com/faq
So basically if you are sharing an Apple ID, one of you should get their own Apple ID.