Yeah, it makes sense, sadly. The NanoPi R76S has Realtek NICs, but PHC support isn't included into the mainline kernel. The out-of-tree r8125 driver is... let's just say it's not very stable. The in-kernel driver doesn't display PHC at all, so it's not surprising that ethtool -T doesn't show anything.
If you're noticing missing MACs and PHC vanishing after a reboot with r8125-9.016.01, it's generally because the driver and kernel versions don't match. That driver is quite sensitive to the internals of the kernel, and things become strange very quickly if udev or the DT bindings don't match up.
It's also important to note that even when PHC works with Realtek, it's frequently not fully developed. For example, timestamping could be there, but it won't sync well with ptp4l, particularly when the system is under a lot of demand. So, for PHC accuracy and stability, this board was never meant to be used for serious time sync.
In short:
No PHC support for mainline kernel
out-of-tree r8125 is unstable and breaks easily
R76S hardware isn't very good for precise timing.
If PHC is a must, Intel i210/i225-based NICs will work considerably better for you. Realtek + PHC is like being in agony mode.