Dreadnaught,
I have 2 XM systems, one in each of my PT GTs. My 2003 GT has an Alpine radio with the Alpine XM tuner pack. The antenna is mounted on the roof, just in front of the hatch (see pic:
My 2004 GT uses the stock in-dash 6-disc changer with the XM MyFi. I have had great success with the small portable antenna, but the home and car antennas will outperform the portable antenna. I will be mounting the XM car antenna in roughly the same spot that I used for my 2003 GT. It sounds like we are using the same spot. Remember, the spoiler *could* be causing a line-of-sight issue. If so, move the antenna on the roof towards the front of the car about 6-8 inches. That should solve your problem. If you don't like the positioning, move the antenna back until you receive a satisfactory reception/aesthetics compromise.
Also, you can change the FM transmitter station on the SkyFi2. Maybe there is a better transmitting station that doesn't interfere like the one you are using now?
Scott