You need to check ‘Enable Asobo Unique ID extension’ option when you export the GLTF file for your mesh livery, but it seems that this option is only available with the official Asobo GLTF plugin, and the newest version (1.3.1) is not supported by Blender 3.6. Moreover, submodel merge is relatively a new thing, which is only supported natively by the ATR at the moment.