high level ins allow you to add an amplifier to a system not really designed for an amplifier. Factory HU's rarely have RCA outs, but since there are speakers, there is obviously a high level input available.
That said, RCA is THE best choice without question. High-level inputs are very dirty and the extra volume is simply distortion. Aside from that, if you have an aftermarket HU then you're giving up an amped channel to run your amplifier - just inneficient.