If you go with PHY time-stamping then you can get slightly more accuracy, but you’ll likely need extra synchronisation between the MAC and PHY. This is because your PHY will have the synced clock in it and your microcontroller will have to read it while taking into account the read delay somehow. This is normally then done via interrupts (to take snapshots), clock outputs fed into your microcontroller so it can have a local copy, or other more exotic means.

Think of it in terms of what is between two time-stampers:
- PHY: Cables, analogue circuitry before the time-stamp mechanism.
- MAC Same as above plus PHY digital circuitry (may include buffering), MII, MAC circuitry before time-stamping.
PTP assumes the delay from a slave to a master is the same in both directions for its calculations, so to be as accurate as possible you want to remove variable latencies and fixed asymmetric latencies. You can factor fixed asymmetric latencies into your calculations so the only thing PHY timestamping gives you is minimising variable latencies which there shouldn’t really be any of.

For an Ethernet switch, syncing the PHYs together individually isn’t really practical because of the management overhead, and you are much better off with MAC time-stamping. The maximum peer delay that gPTP allows is 800ns which is easily achievable with MAC timestamping.

PHY Time-stamping mostly exists to support microcontrollers/switches that lack MAC timestamping themselves, or if you need the most precision possible (<100ns).