Do not want to teach people how to suck eggs but this is how I see it. As the loop is in the carpet below the car then the PT or transponder needs to be as close to the loop in the car as it can get for a good signal. This car has a good layout for a PT as it has only the lower deck to get through and the upper deck if there is a loop on a bridge.
With handouts and a PT the transponder really should have the clearest view it can to the loop. So the position should be chose so as to have the least amount of car in its way.
With a PT bear in mind that with the power drain going to the motor that the BEC in a ESC can have a hard time and I would recommend always using a 4700uF 10v capacitor on the power supply to the receiver just in case (get them from Maplin electronics VH57M £0.61), and always have a capacitor if using the higher drainage 2.4GHz receivers. Or the MRT Bug booster is good as it can supply power for upto 3 seconds if the power goes. I know it is a pain to have yet another capacitor or device on the car but as Tesco says "Every little helps"