You MUST use clamps on the 1/4 tubing because the nipples are actually too small for 1/4 tubing. It's optional with the correct 5mm.
Auto parts store does want to stock two items when people will buy whatever they stock. It's up to the buyer to find the correct parts.
Lots of people jam square pegs into round holes.
I've no idea what the 3 nipple valve does. It's not stock on any CB500/550 I've ever seen. But, as you are doing, people will put whatever parts on the bike they happen to like at the time.
Cheers,