I'm in the Space Age progressive with four 5 team divisions. The current format for this type of league allows for the 4 division winners to make the playoffs.

We'd like to allow a third team in each league make the playoffs as a "wild card." Then have the winningest team get a bye for the first round in each league.

Is anybody aware of a way to customize these options?

I don't know how youd add an extra round. You could try asking admin to see if its possible. I know they can modify the playoff teams but I would be surprised if they could add another round.