My YubiKey requires me to enter a PIN as well, which expires after a period of time. I don't see any significant benefit to requiring a tap after I've entered the PIN.
The PIN can be entered remotely, or indeed supplied by software independent of a human's presence. The tap, on the other hand, cannot be synthesised without a bunch of extra malarkey.
If your Yubikey had a PIN terminal, it could treat the entry on its own PIN terminal as presence indication, but it just discerns the PIN via CTAP from the host computer and that might be caused remotely.
