Envoys cannot send Goodwill missions to Minor Factions that are aligned with enemy players.In a hostile environment an Envoy can use its 'Diplomatic Immunity' ability to secure the approach but its a limited duration ability so make sure no 3rd party enemies are there to disrupt you.By default Minor Factions are hostile to you but you can use an Envoy's Goodwill mission to convince them to join your side.Each Minor Faction spawns with a set of ships, structures, surface infrastructure, and powerful new abilities.
Every game will have a different combination of Minor Faction types and locations.