Alright so I spoke with chad via their online chat:
For the priming step, should i be doing that with the flush valve open or closed?
Chad: That's a great question. When you first turn it on, you'll want the flush valve open to flush the membrane for a few minutes, and you're good to start making water.
you: Per the instructions, you are supposed to "prime" it for an hour before the first use..
Chad: yeah, this is to play it safe, though in most cases, just a few minutes is fine.
you: OK, but for the first prime, for an hour, should the be run for an hour with the valve closed?
Chad: You're just flushing any dust out the waste line so it doesn't clog the membrane.
you: Alright. The instructions are confusing on this point.
Not the clearest answer ever, but I'll take it. I ran the unit in normal operation for the first 10 minutes after flushing for an hour. Outgoing TDS is zero, so I'm good with it.