iwlwifi: pcie: refactor cmd_in_flight set/clear code

A following patche will use trans_pcie->cmd_in_flight
for reference accounting as well. get ready for it.

Signed-off-by: Eliad Peller <eliadx.peller@intel.com>
Reviewed-by: Johannes Berg <johannes.berg@intel.com>
Signed-off-by: Emmanuel Grumbach <emmanuel.grumbach@intel.com>