You need to understand how the system works. The materials in blender are only a representation of how they should look in the sim. You can't manipulate the shader node directly. There is only a one way link. MSFS Panel to Shader Nodes to renderer. If you used the Surface panel the variables that matched got updated, like albedo colour, metallic, roughness scale. The Comp image texture is a special texture where RGB hold three different mappings, AO, Metal and Roughness. These image textures are split up and combined to input to the BSDF node. The renderer then shows you how it will look in the sim. If you don't "use" the same node structure as the exporter requires then these data variables that get written to the gltf are not set correctly and what looked fine in Blender does not work in the sim.
The MSFS Materials have ASOBO extension data variables associated with them. In the early days (Blender 2.7 2.8 2.9) it was ok to use the surface panel for PBR texture etc. The variables in the surface panel matched up to the variables needed for the sim.
As the sim grew and the exporter was updated, Blender was updated. Things no longer matched.
So unfortunately, you will have to redo all your materials and set the proper values in the MSFS panel.