I only swiftcast Flare when convert is up or when multiple targets are to be flared. I personally have noticed that you lose DPS when you do that. I think the reasons are:
When you use transpose, not always do you regen about 1200 mana instantly
When your mana has regened 1200 and you use thunder II and Fire III, the Fire III takes a long time
When your Fire III has been cast, sometimes you have 2400 mp instead of full mp - you could wait for another tick, but that is pure time loss and as a result DPS loss.
I honestly think that doing that results in a DPS loss because it interrupts the casting flow more than it should be. I'll try it out later though (once more)