Re: Product Filter Module and Product Specific Attributes
I think you will have to switch to class-specific/global attributes only, otherwise (even if you find a way to hide the second drop-down via a custom module) someday the product-specific and global attributes may go out of sync.
Class-specific attributes don't share the list of values among products of this class. So, for example, you may have a product having 3 color options, and other one having 5 colors. However, it will be a single attribute, so Product Filter should work properly.