I don’t know of a way to automatically set those material properties on import, but more important in your case is, you’re going to want to consolidate those materials down into far fewer ones.
Having 6,000 materials in one project would be extreme, and would make compiling materials in your project take a very long time. (Each new material that is added increases the time it takes to compile every material in your project.)
The intended way to use materials in UE4 is to have a handful of “master” materials, and create material instances from those master materials. This workflow not only avoids the material compile slowdown I just mentioned, but is also a faster way to work because previewing updates in the material instance editor is practically instantaneous, unlike making changes to a base material asset.
At the very least, I suggest you read up on Instanced Materials in the UE4 documentation. Maybe also check out this video on the Unreal Engine YouTube channel about using instanced materials. (Actually, it may be valuable to watch multiple videos in that “Intro to Materials” series.)
In general, I recommend finding a solution that allows you to maintain as few master materials as you can, and create only as many material instances as you need as well. Likely this will mean you won’t actually import your materials from those FBX files at all.
Depending on how many meshes you’re importing, it may still be tedious to assign your new material instances to each imported mesh, but you should only have to do this once per mesh asset, and afterward, maintaining the “material look” on each of your meshes will be way simpler and easier.