I saw this somewhere too. But, since I've yet to see HB take a flight point, I assume this feature is not really working at the moment. From the questing profiles I use, I surely would have expected to see it take a few. Always keeping an eye on my toons as I do other things, I'm rather certain it doesn't work.
As far as profile writing goes, there will never be a profile element instructing the toon to take a flightpoint--that decision is the HBcore's alone to make.
Instead, the profile writer stands at point A, and says "I want to go to point B". The HBcore is responsible for determining whether that gap is best bridged on foot, flying mount, or some combination--for example, via flying mount from point A to source flight point, via flying mount from destination flight point to point B. Thus, the profile writer should specify where to go, but never how to get there.