As far as I know, ethernet and the PHY is only activated in U-Boot, if there is a command that uses ethernet, for example tftp. Normally the PHY should be brought back again to standby mode when U-Boot stops. Again it is only activated if Linux activates the port, e.g. by an ifconfig up. Unfortunately, the regular Yocto configuration always starts Ethernet automatically. Maybe this can be avoided by shutting down the appropriate service with systemctl.
So if no-one starts Ethernet in U-Boot and no-one starts Ethernet in Linux, the PHY should be rather deeply in stand-by.
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