The Godot importer for 3D assets is pretty bad honestly. It never does what you want.
The way to fix this, is to double-click on the asset, choose "Open Anyway" and then save it as a new Scene. In this scene you will be able to edit the material or change settings.
Then in the material, click the Save As button, and save it with a name. This is required, as you will have to reapply it if you reimport the asset.
Honestly, it seems like no artist ever used Godot or even tested this stuff, because the workflow makes no sense at all.