e1000: handle manageability for pci-e adapters at PHY powerdown

When powering down the PHY (if WoL is disabled) we should only check
copper PHY's and handle PCI-E adapters differently.

Signed-off-by: Bruce Allan <bruce.w.allan@intel.com>
Signed-off-by: Auke Kok <auke-jan.h.kok@intel.com>