[FKHeath]

Several observations:
1. My RAV4 came without the cross bars. Mine looks exactly like your pictures, i.e. there is no bolt or seal on the threaded hole, thus it can be assumed none is needed. (I don't know how Toyota keeps water from going inside, but I don't have a problem after many car washes)
2. The factory cross bars are never attached at the factory, rather they are installed at the port, the distributor or the dealer. When installing the cross bars, the installer should put the covers in the glove box with the instructions sheet.
3. Many people have complained about leaks from the roof rack. (I don't have that problem so far).

My conclusion would be to follow the instruction sheet that should have been included with the covers in the glove box, which is just to put the covers back on when you remove the cross bars.