Thank you for providing so much information regarding your issue.
I'm actually pretty sure of the reason why this is happening. There is a performance optimization "blockMaterialDirtyMechanism" being used in the plugin which will under certain circumstances (camera not looking at the mesh for example) prevent materials from being updated correctly.
Some actions that relate to materials already disable this briefly so the changes can be applied. "Set mesh texture" currently does not.
However that will change with the upcoming update and I'm fairly confident this will solve your issue at least partly. I'm not too certain about the layout change problem you're describing and what actually happens there.
So in case the upcoming update doesn't fully fix this issue please do provide an example file.