You have to sustain in-flight flapping, if you want to sustain flight; whereas the take-off flap is a short burst of activity during which you can go anaerobic if necessary. The difference between a sprint and a marathon.
Albatrosses are a good example: they're pretty hopeless at getting off the ground without a head-wind, and sometimes have to give up on one take-off run and have a rest before making another attempt. They can get stuck on the surface at sea, sometimes for days, if the wind drops while they're in the water; and they flap only very rarely while in the air, spending a lot of time looking for lift by dynamic soaring in the rising air displaced by the front faces of waves.
What this fella seems to be saying (as far as I can make out from the link) is that the pterosaur, with worse wing-loading than an albatross, couldn't get into the air without a head-wind, and couldn't gain altitude by flapping without some source of rising air.

Grant Hutchison