its fine to use the motherboards 3 pins for your fans. it is why it is there. unless that fan is taking up the cpu fan spot(which is usually a 4 pin connector)
the strategic reason why case companies make the front fans molex connectors is because its the closest to the molex cords from the psu when bottom mounted. it saves you the mobos 3 pins so you can instal more fans if you wanted to.