Solar Branch Connector OK under panel or exposed?

So long as the wire is not going to be flapping around in the wind as you drive, I don't think it really matters where it is located. Whatever seems tidier and gives the most flexibility for maintenance or repair if needed would be my choice. Cutting the wires to the proper length is also a good option (assuming you can make proper terminations on at least one end of them--which isn't too hard if you're going to a screw terminal or wire nut or something of that ilk).