A flameout addition does mean you add the honey at the end of the boil before you chill. The later in the boil the better but I don't think it matters too much because you have correctly identified the main problem with using honey: 90% of it is going to ferment out, drying out your beer and thinning it out with only a tiny flavor addition.
Many people add it after initial fermentation or even to a secondary and rack the beer on to it. The main idea here is the later you add honey during the process the more likely you are to get the flavor from it. On the other hand, this is a ginger ale recipe and the honey might be seen more like a sugar addition and not really used as a flavor addition. If this is the case, and it looks like it is, I tend to add my sugar additions around 30 minutes. Thats just me but the recipe is a winner...literally, so it looks like going by the guidelines will give you a great beer. Hope this helps