Those don't care about the protocol as they can provide hardware timestamps for all received packets.
Other popular NICs like the Intel X540 or XXV/XL710 are limited to timestamping of PTP event messages in order to limit the rate of timestamps which needs to be handled by the driver. For those chrony supports an NTP-over-PTP protocol which forces the hardware to trigger the timestamping by wrapping NTP messages in PTP.
Sub-microsecond accuracy is certainly possible. Here is an example with 3 network switches: https://chrony.tuxfamily.org/img/client-hwts-3switch-f323.pn...
The accuracy is limited by asymmetries in network switches.
In any case, whatever algorithms Clockwork is using with their protocol, I'm sure they could be used with NTP too. If additional information needs to be exchanged between the hosts, extension fields can be specified for that.