Ah, no problem, totally understand the issue. I was in the exact same situation a few years ago and had to interpret between modellers unaware of MS flight sim nuances and a fairly prominent developer.
I really don't recommend direct editing of the gltf file, unless absolutely necessary. There are a few ways to address the issue, but I think even the simplest one, that isn't necessarily the most efficient, of just using two instances of the same material, one instance transparent in blend mode for glass, one instance opaque for the other parts, would add a draw call, not require editing of geometry, so conceivably could be done via editing the gltf, but would probably be too complex and more reliably performed through the export settings of the 3d modelling software.