The .gpx exports from my rides (which still contain all kinds of pause data and all points) vary between 50-500KB and Id be suprised if the handset is uploading significantly more than that even if you do upload the exercise over data rather than waiting for wifi. So probably thousands of logged rides a month, or hundreds everyday to use up your limit singlehandedly. Some apps might have features which are data heavy, but I havent really seen any - I dont think live tracking uses much. You could get a free net usage app and check the usage before and after a ride if you want to be safe, but as I also have a 700MB data allowance I dont even consider gps tracking when i think of how much Ive been using.
The warning is just the App using Assisted GPS, where it gets assistance from the cell towers youre connected to which makes the tracking a little more accurate and helps eliminate rogue points, but still relies on your GPS. Some info here if you want to understand it better.
http://en.wikipedia.org/wiki/Assisted_GPS The wifi option though will probably eat your battery if its constantly scanning for open wifi networks, you can probably just turn wifi off before your ride to fix that - works for me.
The better the line of sight to satelites the better the accuracy, but a pocket seems to be fine which is where mine usually is. If it rains heavily ill sometimes transfer it to my waterproof saddlebag and the signal is always a bit poor, possibly the rain, possibly the position im not sure, probably both.