Here's how I envision this:

When a user is prompted to enter a recovery code, Proton Pass could autofill a random code saved in the slots—or when a user is in need of a recovery code, they could manually generate a random recovery code from any available slot and copy their code to their clipboard.

Users must manually enter their recovery codes in Proton Pass. An option to automatically remove a recovery code when used can be toggled, and will be enabled by default.

I personally think it'd be better than saving recovery codes in notes, and it allows more personalization.