Exported mesh is built against reference pose of armature and mesh objects, not that you see in blender.

In qc there might be $definebone lines that re-define reference pose.

What does your QC file look like?

My qc is very minimal while I learn and troubleshoot this. There are no definebones instructions, and I've excluded all animation actions at this time. Will I need to add my own definebones statements? That would be very difficult to get the correct measurements manually. I'd hoped their locations would be exported from blender.

QC....
$ModelName "nf/vehicles/air/falcon/emp_nf_falconjet_mobile.mdl"

$Body airframe "nf_falcon_airframe.smd"
$model fanstar "nf_falcon_fan_Starboard.smd"
$model fanport "nf_falcon_fan_Port.smd"
$model fantail "nf_falcon_fan_Tail.smd"
$model cannon "nf_falcon_cannon.smd"

$SurfaceProp "metal"

$Contents "solid"

$CDMaterials "nf\vehicles\air\falcon\"
$sequence idle "nf_falcon_airframe.smd" fps 1

$keyvalues { "prop_data" { "base" "Metal.Large" "health" "100" } }

And a typical sub model smd file (minus all the triangle data)

SMD exported from blender...
version 1
nodes
0 "base_bone" -1
1 "TailFan_bone" 0
2 "PortFan_bone" 0
3 "GunTurret_bone" 0
4 "StarboardFan_bone" 0
end
skeleton
time 0
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 -0.484572 -4.589298 0.473971 -1.571133 0.016496 0.016484
2 -0.137782 0.513171 3.614685 0.016491 -0.015916 1.570524
3 -0.130809 3.063153 0.001382 -0.006179 -0.001194 -0.349016
4 -0.267483 0.511181 -3.588485 0.016483 -0.000209 1.570783
end

Multiple $model statements are not allowed, use $body instead

And you mentioned (one) exported SMD while there are multiple smds in qc...

Multiple $model is allowed.

Yes, multiple SMDs but I only posted one as example since the others where near identical. And yes you can compile with multiple models. I tried a body group as well which works too. But produces same bone position problem.

I suspect I'm not setting up something in blender to studiomdl's satisfaction, but at this point I don't know what.

If you want, you can upload the files somewhere so we can take a look.

Thanks for the offer, but I think I was able to solve the bone position issue finally. I found my armature rig was at a different scale (56.0) than the reference mesh (1.0). While in object mode I was able to choose the armature, CTRL+A and "Apply the Scale" which returned the scale back to 1.0. I can now see each highlited bone in the correct locations after the complie. I still have an issue where the additional models are not alligned with the bones though. That is a separate issue probably solved by the correct qc entries.

That's what I refered as reference pose. One with un-applied transforms