GPS is a very low power signal and the higher the antenna the better the accuracy. The antenna will acquire more satellites as it's view of the horizon increases. I suspect the average marine receiver wouldn't notice the difference. If you have an unobstructed view you will find the rock before the rock finds you.
The GPS satellites orbit altitude is about 12,500 miles. A few feet of mounting height difference for your antenna isn't going to make any difference. I've been surprised at what the signals will shoot through but it'd make sense to have them have a clear view.
Radar manufacturers suggest that GPS antennas are mounted above the radar array.