I have an exhaust leak at the wye connection in front of the two mufflers. 1) why have two mufflers at all, and 2) can I just replace the one muffler with a longer inlet pipe that skips the wye connection?

I would not eliminate one of the mufflers. Subaru designed the vehicle to meet emission standards and changing the configuration of the exhaust system may not allow the vehicle meet those standards. I would take the car to a muffler/exhaust shop and see if they can repair the leak with a weld.