Hey Brian, that's an interesting analysis, and I agree completely that (a) Medium should be more transparent with the factors that affect our per-minute payout, and (b) the new referral bonuses will inevitably degrade the payout for reading time, unless they're coming completely out of Medium's share, which would surprise me.
As for how Medium calculates the per-minute payout, there's another wrinkle you didn't mention, which is that the payout appears to be massively different if your article goes viral. Here's the proof and my estimated calculation: