The book goes into detail about what the explorers start with in terms of Personal weaponry and their Dynasty flagship, however what about dynasty assets. By that I mean troops, bodyguards, possible vehicles, ships available for background endevours etc.. Should we even bother tracking this or it it just unnecessary bookkeeping that I have to do, and leave it semi nebulous.

How do you deal with this situation.

May party started with just one ship. The RT has 4 bodyguard (elite trooper), and no backup. Everything they had now. they earned or steal it or kill for it...

So don't brother yourself with this stuff. If they want something there is the Acq. system and the Background Endeavour system in ItS.

Assume the ship has the bare minimum it needs to load up from primitive planets, or deliver the Lord-Captain to a dinner date. i.e. One Lighter, one Aquila Lander, maybe a fighter for escort.

one tenth of the crew are armsmen, and one one-hundredth of the crew are officers, but their stats and equipment are no better than the crew rating.

Anything fancier than that, you have either acquired at the start, when you were stating out your ship with Veteran Crew, or Stormtrooper Barracks, or purchased/stolen/looted later in the campaign

As far as other ships belonging to the dynasty go, if any, assume they're all too busy servicing contracts back in the Calixis Sector to accompany the Lord-Captain into the Expanse, unless you want to go to the Profit Factor expense of creating more, and thus abandoning contracts.