It was a design choice that has a number of benefits, and virtually no negatives.
A couple of major reasons...
The RV-12 was designed to meet the LSA requirements, to be flown by a Sport Pilot. By design that means a simple to fly and operate airplane.
Having the pump always operating removes one item that a pilot can potentially forget. Numerous RV-12's have already been crashed because pilots forgot to latch the canopy before take-off... and then forgot to fly the airplane instead of concentrating on the canopy....
The optimal fuel for the Rotax engine is premium auto fuel. It typically has a higher vapor pressure than avgas which makes it more susceptible to vapor lock. A boost pump near the fuel tank, pushing cool (compared to the engine compartment) fuel to the engine, vs just an engine drive pump sucking fuel the entire length of the fuel system, can help to greatly reduce the possibility of vapor lock. This is the same reason most cars for many years have had a fuel pump located in the fuel tank.