You can use short-lived tokens, or you can use long-lived tokens. A long-lived 128 bit secret is superior to a username/password, for reasons explained elsewhere on the thread. So if your short-term token scheme requires programs to occasionally deploy the root account's password (or really any password that a user had to come up with), it's flawed.
Right - I agree that deploying a human-used password is not a viable option.
I'm thinking more in terms of deviating from your described solution on storing keys (particularly long term ones), by storing them hashed (and thus require some kind of account identifier prefix in the Bearer token string).