ARM: tegra: apalis_t30: annotate/clean-up pcie controller/port nodes

Annotate PCIe port nodes and clean-up PCIe controller/port status' with
respect to carrier board vs. module level device trees. As port 3
connects to the on-module Gigabit Ethernet MACPHY it is always enabled
together with the PCIe controller itself.

Signed-off-by: Marcel Ziswiler <marcel.ziswiler@toradex.com>
Signed-off-by: Thierry Reding <treding@nvidia.com>