Argon start for instance having split and paranid plot not accessible (concluded), with reputation very low with those factions, etc. A pirate start that makes impossible to acquire blueprints or buy ships from big factions (in my galaxy I revamped pirates a lot, with their own shipyards), so on.
Everything is quite easy to recreate with the custom start's features, but one thing remains: the HQ. Everything requires it.
I thought about these solutions to make it not the central hub of everything:
1) Making it not owned by the player, so having some basic functions and no productions, hosting Dal and Boso
2) Giving to the player but limiting the nr. of modules one can add. Just a research center, not an industrial hub. And/or maybe only for ship production and personel training
3) Removing it allthogether and placing Boso and Dal on board of a ship? (thou this would remove any research too).
This would require altering md's scripts a lot, which is not realy my daily bread

Any hint what would be the doable solution? Maybe another I did not think about..