According to
http://wiki.feed-the-beast.com/Pollination, "gui.maximum" pollination bees have a 99% chance to plant a new flower. I assume that's per bee tick (27.5 (?) seconds). But since Aura Bees are kind of "end gamey" you'd probably only have a 25% chance (from Industrious bees) at best (I would always breed Aura bees before any of the relatively useless bees that have between "Fast" and "Maximum" Pollination, except Windy obviously, but you could pick up Rural or Monastic for a slight boost fairly easily I guess). The "Fast" speed should give about 1 flower every ~110 seconds per working queen.
What I would do is just throw down an upgraded Harvester. I assume flowers in pots are safe from it, but they still allow your bees to work. I might actually try this some time. If it works alright I can spend less time on early power generation and more time on bees.