I discovered that because the Bluesky App still uses legacy authentication, this bypasses the 2FA settings.
Bluesky has an email 2FA verification feature, and I think we can develop a compatibility shim based on this. That is, when the account has 2FA enabled and attempting to login via legacy API, the system will send an email containing a verification link to the user's mailbox. The user can click the link and complete the TOTP verification to obtain the email 2FA verification code to be entered into the Bluesky App.
Prior art: https://tangled.org/baileytownsend.dev/pds-gatekeeper