I am not sure why you keep rendering, but there is no reason to export a file. A separate sequence is just as easy if not easier. Render when you need to, not just for the heck of it.
If you need to fade in and out, you might find it faster to razor the ends off so that only the part of the clip that matters needs to be rendered. A single ended transition might be easier for you.
I am not sure why you have premultiplied with black in the first place. I export Quicktime Animation when I export files with Alpha channels from After Effects. Sure it is premultiplied but with no color below it (the background color of the comp does not count) there is nothing to premultiply with.
Premiere Pro does not render per layer, no. Only export to DV AVI uses preview files. That will not work with a 32 bit file.
In any case, I suggest fading in and out in AE not Premiere Pro. But there is nothing you can do to speed up keyed footage for render or export to my knowledge. There are hardware devices that help, but not software to my knowledge.
If you had a recent vintage (2007) PC, you would probably be a lot happier. The speed of a Quad Core (or two of them) processor speeds things up considerably.