One way to solve the problem might be by introducing ways for players to gain permanent access to a planet. Those should be hard to accomplish, probably somewhere in-between the difficulties of the Abomination and Angel transformations. Maybe by gaining the favor of a certain God - a Good one for Arboreus, Neutral for Syndesia, and Evil for Tartaros, and then gaining an invitation from a guild that's based on the planet in question.
If this were to be implemented, I think there should still be some sort of incentive for single-race guilds, maybe by making their guild member limit higher than that of mixed guilds. Otherwise, there'd be no point in making a single-race guild, since you'd only limit your recruitment options and not gain anything. Taking that thought further, maybe there should be a separate category for bi-racial guilds (ie. Humans and Beastmen only) and truly mixed guilds, with the latter gaining the biggest penalty to their guild member limits.
And to make sure very few people take advantage of these options, in order to preserve Fractured's "Three Races - Three Gameplays" philosophy, even if you manage to gain permanent residence on a foreign planet, there should still be penalties for doing so. Maybe not necessarily combat-related ones, but maybe crafting and studying should take significantly longer.
