It's a weird relic of MLS history.

Typically, in European Cups the semifinals are two-leg affairs - home and away.  Then the final is in a neutral location, so you only need one game to be fair.  Since the game is important culturally, people travel.  Even neutrals will be interested and buy tickets.

So MLS did the same thing historically.  The championship game was in a neutral location.  The only thing was that people tend to follow their own team not the league as a whole in MLS, so the championship game wasn't a hot ticket if the local team wasn't playing.

They changed the rule so that one of the participating teams hosted.  Should they have also changed the format to make it two games?  Probably.