Switching a RAID between manufacturers is almost certain failure. Although, it "should work" companies often place a header containing data about the RAID there and these headers are different. However, backward compatibility within the same company usually works. For example going from a Adaptec 3805 to adaptec 5805 should work.
You could plug in the exact same mobo and it would work. A different mobo with the same raid controller might work.
The built-in RAID controllers general use the CPU to do there work instead of any independent CPU.
Hardware RAID controllers are entirely self sufficient and have there own dedicated CPU on the card. These cards are generally faster and have features that make them way better. Also if the motherboard goes you just plug the hardware raid controller into the new motherboard of any make/model and go. If the hardware controller dies replace it with the same or newer card and you should be fine.