I store them in the same password safe for quite a simple reason; more convenient and less complexity.
I personally see TOTP only as a security against phishing and password stealing attacks. I don't see how a separate database for TOTP secrets improves on that in any way.
The thing is; a Keepass Password is (usually, looking at your password requirements Paypal) fairly secure in of itself, long, random and contains all the good characters.
TOTP is mainly useful when you have weak passwords and enter them into the wrong place, something that Keepass (especially with the Browser Extension) fully prevents. It's just for show and some extra padding.
Though I do use U2F anywhere I can.
