How would you apply a pea-size amount unevenly? That makes no sense.
Anyway, the point is to fill the gaps to improve conductivity. While spreading a pea-sized amount with the heatsink, it conforms to fill the gaps between the CPU and heatsink. The purpose is NOT to push it flat, but to fill the gaps. It's also not about applying too little or too much. If you spread it yourself, you may not accomplish that. Applying too little or too much are both bad. Thermal compound is not a better conductive medium than direct connection between the heatsink and the CPU. It only improves the places where there are gaps. If you manually spread it too thinly, you may not accomplish filling those gaps. If you spread out a thick layer, then it's a mess to clean up and performance is poor because that whole blanket of thermal paste will act an insulator. Again, metal to metal is a better heat conductor than through a blanket of thermal paste.
The only places you need thermal paste is for dents and scratches between the two surface. Spreading them out doesn't conform to the proper shape. I hope that helps.