How do you prevent malware running on the pwned laptop from asking for an ephemeral cert to be issued? How do you know a human being is in the loop? Usually ephemeral sessions are up to 15 minutes (also to deal with misaligned clocks and unhappy users) - plenty of time for malware to ship the cert back to a command-and-control server.

This is the key advantage of hardware keys, the fact that the physical press is required prevents the keys from being exfiltrated from the machine by malware.