When you're using hardware raid, server is able to read HDD temperatures and adjusts fans accordingly. When you're using AHCI, server can't read HDD sensors and turns fans higher. I'm not sure why it's implemented this way, but you can easily check it via iLo web interface. For me it's 20% fan vs 6% fan and I can distinguish it, I can hear 20% fan at silent night, but 6% fan is really silent, so my wife can sleep well.

If you don't have those problems with noise, it doesn't matter (and I would recommend to avoid those "hardware" raids, I have much more trust with widely used open source solutions).