msm: ep_pcie: Apply gpio settings based on the device tree flags

Read the device tree gpio flags for all the pins but apply
them only for the MDM2AP_STATUS in order to support boards
that require an active low signal.

Change-Id: Ia1972b4b9046ff947864b7a31781919a31396ae0
Signed-off-by: Gustavo Solaira <gustavos@codeaurora.org>