Assuming this is the same as I received with my console several months ago, the small plastic piece is not a cover for the charging dock - it is a REPLACEMENT for the charging dock.
If you decide you don't want to use the iPhone or USB dock, you can disassemble that portion of the console (requires a screwdriver and only a few minutes), remove the iPhone/USB dock plastic piece and the USB charging cable, and install the blank plate to completely remove the smartphone charging feature.
What would be useful would be for Tesla to provide several of these pieces with each console and make them available in the Tesla store. The kit should include the blank plate, plate for the charging iPhone/USB phones without a case (which is what Tesla provides with the console), and a second iPhone/USB plate that has been adjusted to support charging in a typical phone case. Plus, because the dock assumes a specific form factor for the charging cable, the cables should probably also be included.
Buying the kit would provide support for a broader range of today's smartphones and eliminate the manual adjustment that are required now for when smartphones are being used with cases.