Welcome! That warning is a hangover from the Vision+. It doesn't apply to the Phantom 3 and the warning will not be there anymore in the next release.
You generally want to be flying at least 3X higher than the highest feature you are mapping. 4 to 5X is better. You have to make the tradeoff between GSD and being sure to get good data.
You won't have to wait too long... We are currently beta testing our Map Pilot App for iOS
You can certainly fly freehand in the meantime but be sure to get plenty of overlap. You will likely end up taking way more data than you need.