Think you might be out of luck with this one.
All models (.MDL files) have a centre position. 0,0,0.
Within the MDL file each part has its own axis which is offset from that centre position. And within every part each vertex is offset from the parts axis.
The viewpoint in the aircraft.cfg is also an offset from the 0,0,0 position so changing that will only alter the eye position and not move the model position at all.
Changing the reference datum position will also not move the 0,0,0 position. The reference datum position is just a way for a developer to enter the real world reference datum position (which most likely will not match the standard flight simulation center point) and then enter positional data directly from plans without needing to convert the datum position.
According to the SDK the location of the centre position is the "standard Flight Simulator center point, which is on the centerline chord aft of the leading edge."
No mention of how high or low to set the centre point though so you can get different interpretations of this position which leads to your issue.
If the position of the centre position is different between your exterior and interior models then as far as I know there is no way to individually adjust that centre position using aircraft.cfg or .air file tweaks.
You can use Model Converter X to load the MDL and that can move the model around relative to 0,0,0. This might be interesting to see exactly how far off the two models are by loading both the exterior and interior models and comparing their positions.
But unless you have the original modeldef.xml you can't export your changes to make a working MDL file.
You could, in theory, hack the MDL file with a binary editor to change the position but this would involve a lot of hacking as you would have to change each parts position (and there could be hundreds of parts).
