Have you trued using an AppearanceSetter?

If your FBX files already have an appearance then it’s a bit tricky to modify an existing appearance but it is still doable.

It’s fairly straight forward to do this with an ApprearanceSetter  

Hello

The initial geometry is a surface.

I used the "AppearanceRemover" first, then the "AppearanceSetter" and wrote both an fbx and an obj file for testing.
When viewed in the inspector, the obj file is transparent, the fbx file unfortunately is not (refer to attachment).

Hello
I have found the problem.
In the parameters I set the parameter "Embed Textures" to “No”.
By adjusting the setting to "YES", the FBX file is also transparent.
So the question would actually be "How do I create a transparent FBX file if I don't want the texture in the file?"

Ahh nice discovery, Thanks for sharing. Sorry I didn’t follow up with you