I'm confused, that seems like it confuses two independent aspects:
1. Whether the TOTP code comes from a fob-device versus a phone-device.
2. Whether some interactive interface you're using gives you a chance to see/confirm what you're about to authorize or not.
A phone app can lie to you about the transaction you're about to authorize regardless of whether the TOTP code was transcribed from an external device, transcribed from another app on the same phone, or auto-filled by itself.