I saw Cyclone V and incorrectly assumed that it was the Soc Ethernet mac that was used. The Soc Mac supports hardware timestamping but not timestamp insertion in the packet (which are two different things).
I've never used the TSE in that configuration but according to the documentation it will only insert the timestamp in the sync packets in the 1-step synchronization mode, if the 2-step flag in the flagField of the Ptp frame is 0. Is this our case? The forum reduced the size of your snapshot and it's difficult to see your packet contents.