Glass polys:
If by polygroup, you mean a group of polys all connected to each other, then yeah there definitely would be cases where there are more than one of them per subobject - like for separate sections of a canopy.

Subobject properties:
It gets tricky there because we only have 21 characters to play with in the name of the helper. The main two ingame model features this helper would....uh,....help with would be rotating subobjects and multipart turrets - both of which should be off-axis rotation compatible as well.
So, the data that they take is as follows: (this is a little long winded - I'm sorting it out in my brain as I go here.

)
Rotating subsystem (call it a radar, whose submodel is facing forwards)
Movement Type: Rotate [we need a trigger to turn this feature on in the model file]
Axis: Z [we need a way to define the axis in the model file]
Properties:
$special=subsystem [this can be auto-added to the properties if the movement type is rotate]
$name=Radar Dish [this field can be auto-gened from the parent subobjects name. No need to specify]
$rotate=5 [we need a way to define the rotation speed in the model file]
$uvec:0,1,0 [we can get this from the helpers Z axis]
$fvec:0,0,1 [we can get this from the helpers Y axis]
Multipart Turret (pretend it's an off axis one as well and the subobject faces forwards)
Movement Type: Rotate [same]
Axis: Z [same]
Properties:
$special=subsystem [same]
$fov=180 [we need a way to define this in the model file]
$name=main turret [either just grab this from the parent subobject model - it's not used ingame by default anyway]
$uvec:0,1,0 [same]
$fvec:0,0,1 [same]
Of these, it means that the two typical sets of 'flags' we'd need to set in the helpers name would be:
Rotating subobjects: -> Rotate flag, Axis & Rotate speed -> Eg: "Rotate:Z,RotVel:5"
Multipart turrets: -> Rotate flag, Axis & FOV -> Eg: "Rotate:Z,FOV:180"
And I think that'd be about all it'd need to do. There aren't a lot of options that go in the subobject properties field anyway - and most of those extra ones that are there aren't the sort of thing that you'd do in a pre-conversion model anyway, including:
"
$triggered:", "
$look_at:#", "
$detail_sphere:1,#", "
$detail_box:1", "
$box_min: #,#,#", "
$box_max: #,#,#", "
$stepped",
$steps=#", "
$t_paused=#", "
$t_transit=#"
Firepoints:
They could be children of the turrets, but I think that should be more for organisational purposes than a requirement. I think as long as the firepoint helpers are correctly named, their location in the hierarchy should be irrelevant.
