Rich,
Very good points. It would be interesting to see if the 4% signal loss could be offset by placing the antenna farther than 5ft from the panel, thus getting it away from all the rf,static, and electro-noise a panel emits. A 5 foot cord won't allow you get far from the panel, especially if your mounting the iFly on a yoke. It really depends on your plane. I'd also keep the excess wire coiled in a loose loop, just like most of the wires under a certified panel.
You might want to plug the external antenna in and place it in different locations, use the GPS diagnostics page to see the signal strength changes and choose the best location. Just inches around a panel and metal can make a nice improvement of more than 4%. Certified externally mounted GPS antennas are typically placed far from the panel, like on the belly or back of the fuselage to improve signal and reduce the risk of interference. Just a thought. Have a great weekend.
When I mount mine, I'm putting it in the back window of my c-172. There is enough going on around the panel.