You can always turn the FCM service on or off. Most people who are trying to target a subset of their users use Auth (including anonymous auth) as a good identifier of which token goes with which user. It also lets you keep track of which tokens are no longer valid.
If you are not trying to target a user based on their specific usage of your app (you just want a list of all tokens), you could do 1 of 2 things:
1) (recommended) Setup a Cloud Function that takes in registration tokens from your app, verifies them, and then writes them to the database using the Admin SDK.
2) Setup your security rules on Firestore to allow only writing new data to your token list, and no deleting. Also write some verification into the rules (or a on-write Cloud function) to make sure it looks like a token before saving it.
Bonus points if you use anonymous auth and secure your function/database so that a user can only write to the entry for their uid. If your users later login, you can
link it to the same account.