Ideally the document should have the ability to set the size and those settings are respected at prototype export. Ideally the use of px, pt, em, and percent should be available. I really don't feel that the option between 120dpi and 96dpi really adds any value here to me. 96dpi is the defacto standard on modern OS's and no matter what I choose a pixel is a pixel. pt's really are a print measurement and to me really don't belong in the software industry, otherwise you'd also have a 72dpi which is where the measurement was derviced from.
To keep things consistent across all machines it doesn't matter what unit is used so long as the designer is fully aware of what they are doing and at this point to do that, I need a cheat sheet next to my keyboard to make the conversions.
I look forward to some cleanup on this to stop some confusion.
Mark Johnston