You want STRAIGHT alpha in almost every case. Avid, FCP, PPro, AE and every other compositing or editing app I've ever used prefer straight alphas.
Create a custom template using, for example, QuickTime JPEG2000 and pick 32Bit like this.
You'll end up with a straight alpha QT that will work just fine in any app. If you must have pre-multiplied then you have to use the Render Cue and beware of the edges when compositing.
Here's the result of the test render in AE. Note the file interpretation and the transparency.
BTW, you can save the preset (I did) and use it at any time by adjusting AME's preferences.