Wow, this topic has been discussed a lot recently.
To better understand the engine breather, check out chapter 8 of the Honda Shop manual CB500/550.
For the uni NU-4055, it fits both the CB500 and 550 Filter boxes and the 500s don't have the engine breather set up.
The air plenum just behind the carbs has a drain fitting. This hose is a reduced diameter hose that routes behind the engine and in front if the swing arm. The end is open but rather small to allow any gas that might over flow into the chamber to drain. If would be very bad for that chamber were to fill with gas. And back fire could ignite it and ingesting raw liquid into the engine cylinder can bend/break a piston rod.
The fitting at the top of the engine goes to the side of the filter box (NEVER the air plenum chamber). The filter box also has a drain tube at the bottom that is capped. The cap has a slit in it, that is pinched at maintenance intervals to drain collected water condensate.
The bottom of the filter box has the parts you see in the picture you posted. Those parts; gasket, foam element, and metal assembly are there to keep the engine vapors from fouling the air filter element. It will ruin the stock paper element very quickly with oil and water vapors/droplets. The foam UNI type will survive this much better, but the cleaning and re-oiling interval will shorten.
Cheers,