That's what I'm thinking too, use a three tiered set up more throughout the day when most of the M8's are on line. This will become increasingly an issue when Fairfield Metro and West Haven stations open, since that will only further add to the number of stops between Stamford and New Haven. And if you think about it, having a three tiered set up might even save on equipment since the Bridgeport trains would be turning around sooner. This is opposed to having all trains go to New Haven and alternating between trains making key stops and ones making all stops, which seems to be the setup they are mostly using now.
This construction is to accommodate storage of the M8s, as the current setup is pretty useless, but it's also to organize and better use the land available, as with the new MOW tracks to the south. This yard was in pretty terrible shape, and was basically used as a boneyard for old MOW equipment etc, so this allows the track department to consolidate what they need and store it properly. The employee parking free-for-all also looks to be fixed here.
On a related note, you should have seen what they pulled out of here when they cleaned it up to prepare for construction: old tie-handlers and spikers from the 70s left to rot, pallets of old plates and joint bars, and all the trash and debris you could think of. At the least we can expect everything to move much smoother once construction is completed.