Isn't the point of having a centre door so that mingling between entering and alighting passengers is reduced?
Also, the "board-at-flag" policy mainly applies to passengers who are boarding rather than leaving - you should be able to leave while the bus queues behind others. To me, allowing parallel boarding when using this type of vehicle seems to make even less sense. The bus could be obstructing an otherwise empty stop for the 4-5 minutes that you suggest boarding would take.
Unfortunately, the staircase is positioned forward, behind the driver, so there's very little opportunity to separate boarding and alighting passengers.
I'm aware that passengers are allowed to alight before the bus pulls onto the stop but, if it gets a free run, that's not going to happen.
The Enviro 400s are of a similar dimensions to the double-deckers which operate in Berlin - these have not just 3 doors, but a pair of stairs as well. The same layout is true of the New Routemasters in London (which have a decidedly lower capacity it's true). At 129 passengers, the new Edinburgh buses have a capacity not far off the Citaros now banished from London, which also had three doors and, as we know only too well, allowed boarding at all doors.
All of which is to say that these operators have specified vehicles that can get in and out of the stop in the minimum possible time. Perhaps Lothian have got this on their radar and don't foresee a problem, but I'm interested to see how this does all pan out in the hurly-burly of daily operation.