I think the barcode window is entirely for outgoing routing.
When I noticed this for myself, 2007 sometime, I had a common problem where every Nth disc would take an extra day to be received, and that would really throw off my pattern, which mostly was just to have a couple movies for the weekend.
So soon hypothesized that it'd happen on days the barcode was not visible. So to test, I put 1 of them wrong intentionally, mailed all 3 at the same time, and the 1 that was wrong did indeed take an extra day to be marked as returned.
So I didn't have any real facts, just an observation that seemed plausible to me.
Usually the mail delivery between the local Netflix center and my address is overnight both ways, but occasionally it takes two days for an envelope I return to be processed. I've attributed that delay to the post office, however, and not to having two DVDs in the same envelope.
You haven't noticed any extra delay by doubling them up?