All: apologies for any spoilers without warnings. There's plot discussion from story mode in this one, so fair warning.
There is one other factor we could tweak with the reps that would change things. I'd think that if you turned up the "Object Destruction Rep Change" for Nomad ships way high (most factions have it at .03; boost it to 1.00 and see what happens) and kept their Empathy focused against the Order, and the Order's Empathy shared with basically all humanity, you're either with us or against us. Killing Nomads would please only the Order (and nobody else by way of "splash"). Killing anyone other than Nomads would piss the Order off (but not please the Nomads). Killing a single Nomad could set them all the way to hostile again from friendly, depending on the settings.
So you COULD go forth and hunt criminals, and then hunt the Nomads, and then hunt the Order, and then hunt criminals again to get straight with the Houses (and piss the Order off), but if you try to set the Order right by killing Nomads again or buying off Zoners, for instance, you lose all the juicy Nomad benefits because the Nomads get pissed... So no matter what, you'd have to have some enemies, at least the Nomads or the Order (maybe both), and probably a few more besides.
I thought that the main reason it'd be a PITA to get it to work would be because there are places that players shouldn't be able to land... yet. A suggestion if I may as to environments?
I guess that the Lost Battlestar would be the only dockable Nomad port in this edition if you tweaked the reps and didn't wanna fuss with interiors for the Nomad Base or the Dyson Sphere or whatever. Since the Battleships all use similar bar and landing bay graphics (and have a ship dealer), nobody's expecting anything super special as far as the interior environments anyway for a Battlestar: we've got two different series of Galactica and the bays ain't the same on TV. So pick a battleship interior: Rheinland or the Order would be fine. I don't think anyone will whine about it.
The Nomads have infiltrated people in the Liberty Navy and Rheinland Military if nowhere else in the Story mode. So it stands to reason that when the tide turned against them that some of 'em would've made it out, assuming that it was the ships and not the parasites that got sucked up by the super-gate. So you could put a few Liberty Navy and Rheinland Military folks in the bar, and use robot bodies for the salesmen. Maybe in a later edition, you could make a Nomad Asteroid base (steal Cadiz from the Corsairs), say they took it over from the Zoners or someone: everyone inside LOOKS like a Zoner, but when you talk with them... *evil grin* Maybe one or the other places is the off-loading station for humans for new Nomad infestation. The devil is in the details.
Believe you me, I appreciate the level and depth of work necessary to make this sort of thing believable. I DM a 3rd Edition AD&D game certain nights, a scratch-built world a friend of mine started and that I've contributed to over the years and have committed to doing all the graphics work (mainly producing all the maps) for for it to be published. Half of the crap in the game is made up and play-tested by the seat of our pants. Much props to you, Igiss, for finding this medium to express your bad-assitude within, and thanks for all the hard work!