Yes, it does seem to be per engineer. I think it's because it's tracking the git metrics on each engineer.
I'm pretty surprised that the price goes up per engineer as the team grows larger, especially as you're getting serious economies of scale -- all the math and stats is as easy to perform on 400 engineers as it is on 4, once you've got the system in place.
I would assume the "engineers vs accounts" is due to the output not being intended for the coders, but the managers. I.e. you only have accounts for the managers, but you price based on how large a team they are monitoring.
(This is just a guess, I have no connection to haystack)