Hmm, but you reset x-forms on everything else after placement?
Not sure what you're asking.
You're supposed to reset xforms of all geometry before exporting. Whether you want to also reset xforms of helpers depends on whether you need the orientation of a helper for anything; helper orientation and scaling can help you export normals of thrusters, firepoints, glowpoints, docking points and eyepoints as well as the radius of thrusters, glowpoints, special point subsystems and path points.
Personally, I tend to export as much of those as I can so that I need to do only a minimal amount of work in PCS2, but unless you have a lot of normals/radii to set, I'd suggest just reseting xform on everything and setting all the aforementioned things in PCS2. Note that you don't even need to set firepoint normals for a turret which has an $fvec and $uvec.