In a customized faction, you can only choose the planet system (Alterian, Arb, Iconian, etc...), and not the way the planet are designed (layout, hexagons grouping, bonuses, mines/buildings). It is done randomly by the game.
But you can change the leader's logo, foreground and background images, the citizen images, the texts when discussing with this civ, the types of ships, the various colours. But Not the planet.
The building are determined by the game, according to the Ben/Prag/Mal ideolgies, and some special traits.
Unfortunately, even in a customized map, you cannot do much on a planet, using the available tools:
- change its name/all system names
- decide of its type (sun)
- change its basic size
- add any improvements in it, mines, special buildings (from ideologies/traits)
You can NOT:
- choose how your hexs are grouped, or where.
- choose what bonuses (ex: +3 All Constructions) are generated for an hex.
- which hex receives a bonus, or not
If you really want to go deeper, and play with XMLs, here is the guide: