Your annoying problem of textures seems to (IMO) be in relation with LODs/Texture management.
On this screenshot (https://forums.flightsimulator.com/...621712f38104f70ef0c82dc4774af932f5c55fcd.jpeg)
The size of the boat is very small and therefore the mechanism of LODs must be used. There was a discussion about whether or not to reduce the textures with the extra LODs and the person was complaining that the object was turning gray instead of keeping its original textures. One of the solutions was to use the notion of vertex colors for some LODs to gain in memory and rapidity
If the management of LODs remains as it is today, I think it will be necessary to create at least 3 LODs for each ship
As RumbaFlappy suggests you should go and have a look at this type of discussions:
I think the issue is different - the sim engine simply picks textures from a completely different simobject at random. It can be inside the Global AI Ship Traffic or another folder with simobjects - e.g. aircrafts - at one test run everything okay - during the next the texture allocated is from another model... nothing systematic. So far I just observed it for the simobjects included as mdl files - the ones I have converted to gltf works properly... I think...