It's to do with meeting emissions standards. Most cars of the period will have similar arrangements.
One of the small diameter pipes connects the purge valve, for the carbon cannister that traps fuel vapour from the tank, to before the throttle body butterfly valves. That reduces unburnt hydrocarbons.
The other one connects the small spigot on the breather box at the back of the engine to before the throttle butterfly valves. That's burning oil vapour so also reduces HCs. Probably under engine conditions where the two bigger pipes on the Y aren't effective.
Correction.. for 2.6/3.2 and possibly long plenum 3.0:
The outer two pipes, 1/2", are the primary connection to the breather box as a Y tube. This feeds directly to the front of the TB.
The smaller of the centre two, 1/4", is the smaller connection on the breather box. This is the small hole into the plenum from the breather bridge.
The remaining hose, 3/8", is the connection to the purge valve/charcoal filter/evap cannister gubbins. This is the larger of the two holes into the plenum from the breather bridge.
The top hat seal not only seals the breather bridge to the plenum, but also separates the purge valve side from the breather box which prevents a vacuum leak to the intake from the fuel tank.