The reason you don't see flicks used all that much is because media encoding is incredibly proprietary in the space where it matters most, live broadcast. Selling into the broadcast space, every broadcaster has petabytes of video in their own chosen format. You have to support EVERY format to sell broadly, and they're not going to let you transcode everything into your format. Using flicks gives you the ability to support as many combinations as possible with the least effort.

It matters very little when users are trained to tolerate slow transitions between videos, formats, etc...

It also doesn't matter a whole lot when doing offline transcoding either, as you can afford to do the more expensive calculation.