Check is the OverlordContain module has
PassengersInTurret = Yes
This tells it to take into account the parent turret's angle.
Also check that the turret turn rates in the AI module of the parent unit and the portable structure are the same. If they are different it will mess up the angle of the portable structure turret.
Another way is to not use overlordcontain but just have 2 turrets in the parent object. Turret and AltTurret, see the battleship for example.
If the other turret is in a seperate W3D model (a la technical gunner), it should attach to a bone in the parent vehicle model that is not part of the parent vehicle's turret, ie that does not turn.
As for deployable units, why not just use DeployStyleAIUpdate?
See the ChinaVehicleNukeLauncher and AmericaVehicleSentryDrone for examples. You can have the Draw module use different models or animations for the packed and unpacked states, see the nuke cannon for example.
If you want to use the suiciding method, see the teleporting Tardis in my
Laser General mod 1.0, or the laser drone that converts into a laser turret building in my
America Mission 8 for Zero Hour single player mission. Somehow they do not say "Unit Lost" when they suicide.