I'm also sure that it will go up a little also. However, with my other setup, it peaked right above tuning frequency. Also, other Accord owners are reporting around a 50hz peak at the headrest. I know that those measurements are equipment/install specific, but it's vehicle specific as well which has me stumped.
Well, this is my theory, from what you have stated so far:
You have stated that the score peaks at 45hz with both 50hz and 48hz tuning, with the sensor placed at the headrest of the car, and that the frequency that the score peaks at drops lower as you tune lower. From my experience, as you start tuning higher the peak score inside the car will often stay at the same frequency, but if you tune lower the peak score inside the car will drop to lower frequencies. For example, in my explorer I can change the tuning from 39hz all the way up to around 60hz, and the score will still peak at 49hz legal, but I can lower the tuning down to around 35 hz and the frequency where it hits it's peak score will drop down to around 45hz legal. I believe you are seeing your natural car peak frequency at around 45hz with the sensor placed at the head rest. I also believe that you will see a natural peak score at around 50hz with the sensor stuck to the windshield, if you test it. I think you will find that if you start cutting the ports in small increments and testing alot, that your peak frequency is going to want to stay at around 45hz at the headrest, and that you will find a fairly large range of tuning frequencies that it will still result in that peak frequency.
I think the tuning frequency that WINISD is reporting in this situation may be off a few hz, but I doubt that it is a dramatic difference. I have often found by running an impedance sweep than the WINISD figures are off a little, but not much usually.
My best advice is to play with the tuning frequency in the car until you find the results that you are looking for. Use the WINISD tuning results as a reference, and keep good notes. That way if you want to change the setup around in the future, your notes and reference tuning may help you save some time testing.