e1000e: 82579 do not gate auto config of PHY by hardware during nominal use

For non-managed versions of 82579, set the bit that prevents the hardware
from automatically configuring the PHY after resets only when the driver
performs a reset, clear the bit after resets.  This is so the hardware can
configure the PHY automatically when the part is reset in a manner that is
not controlled by the driver (e.g. in a virtual environment via PCI FLR)
otherwise the PHY will be mis-configured causing issues such as failing to
link at 1000Mbps.
For managed versions of 82579, keep the previous behavior since the
manageability firmware will handle the PHY configuration.

Signed-off-by: Bruce Allan <bruce.w.allan@intel.com>
Tested-by: Jeff Pieper <jeffrey.e.pieper@intel.com>
Signed-off-by: Jeff Kirsher <jeffrey.t.kirsher@intel.com>
Signed-off-by: David S. Miller <davem@davemloft.net>