Here might be an odd way of doing it: have certain types of home planets only colonizable by one race (eg. DesertHome by Advent Loyalist, TerranHome by TEC Loyalist), then include only one of both planet types in the map. If you want other factions to still be able to colonize a planet that was a faction's capitol, just have the first fleet supply tech unlock colonization for those planet types (or alternatively, have the unlock tech be free and level 1). Note that this would probably only work on a two player map with two non-mirrorable factions (ie. if someone sets both players to Advent Loyalist, the game will probably crash). The only way to ensure the game never crashes would be to have as many home-type planets per faction as possible players, though this does mean that if not all players are the same faction, starting spots will be pseudo-random for each player (ie. the unoccupied home planets will be randomized).
