The other soundcard is in a box, not connected to the motherboard, due to a lack of PCI slots. I really do no understand the choice of MSI to only use 3. I personally would have needed atleased 5 slots, but could not find any (MSI) bord with 5.
It comes down to a change in technology that is happening, Me27. 6 or 7 years ago you would have found most motherboards with 3 PCI and 2 or 3 ISA slots. Then we went to 5 or 6 PCI when ISA pretty well faded. Over Time AGP came out and took the place of one of these PCI slots since you no longer needed one for graphics.
Now we have PCI Express for the graphics, but the technology for PCI-E has also started to be implemented for many components that were previously PCI only. So now we are changing technology again and you have 3 PCI and 2 or 3 available PCI-E slots.
As time goes on you will probably start to see more and more boards that contain more PCI-E slots and less PCI until standard PCI fades and the next technology comes along.
It's part of changes to technology.