Why are you using networkd instead of networkmanager on a desktop?
What a weird question. Networkd works anywhere systemd works, why whould desktops be any different.
It’s the same as asking someone “why are you using systemd-boot instead of grub?” Because I like systemd boot better and it’s easier to configure. Same with networkd, configuration is stupid simple, I have installed it on my work machine even.
As for op: since you can manually ping ip addresses and the issue seems to be time-based, could it be that your machine is somehow not renegotiating a dhcp lease?
If the time is off by that much after being powered off, this tells me two things:
An incorrect clock can absolutely cause network issues, so I would bet that’s what is causing you trouble