It would definitely make sense for some of the "express" buses to go through the tunnel. The 5PM from Wilton Terrace on Friday didn't get to Busaras until 5.40PM and by the time everyone had got on the bus it was close to 6PM, thankfully the driver went via the tunnel which cut the journey time significantly. Since this bus is full pretty much every day when leaving Busaras the issue of pickups at the Mater / Cabra / Blanch doesn't matter so using the tunnel is the smartest way to operate the service.
As an aside, one of the drivers told me that they have to pay for the tolls on the M3 from the cash float!!! Why can't we have some joined up thinking for something in this country, surely each bus could be fitted with an easypass which would mean the bus could use the express lane.