As per the BleST discussion I started in the BleST Bug Reports on Material uniqueness:
https://steamhost.cn/steamcommunity_com/groups/BlenderSourceTools/discussions/0/3104641620181885419/

Can you add an option to the Decompile screen that will give an option to append something (don't care what as long as it is something short and simple like dupe_ or _dupe) as either a prefix or suffix to a material name if we strip the path from material names?

Edit: In fact thinking about this, a 3 character random on the end might be better (maybe??) The problem is still going to exist if importing multiples of the same decompile, but it would be limited to to that model.