The 200 inhabited systems per sector is something I've seen bandied around on this forum, here and in the DW and DH threads. I'm not owning it. I do think it's close enough to perform number crunching with.

there never seem to be enough Astartes to go around

In part because some of the Space Marines deliberately choose to continue sitting around for a better opportunity to prove themselves, it seems!

Like the ones who won't do a thing unless they have consulted the imperial tarot and the omens are good.

Oh they're ever so rare... Unless you need some for story reasons, and then they'll be available/show up at a thematically appropriate time.

The trick, like with most stuff, is to not over-use them, or have them eclipse the PC's in importance/doing the cool stuff. Beyond that, I say go right ahead and come up with a reason for them to be wherever you want them to be.

As extra information, the Deathwatch supplement "Honour The Chapter" specifically states that the Marines Errant have a relationship with the Rogue Trader House Ecale on pages 42 and 43. One specific sentence indicates "To this day, there are always Battle-Brothers of the Marines Errant Chapter operating on detached service among the vessels of House Ecale." The book portrays this arrangement to be an ongoing mutually beneficial arrangement; in another supplement it is suggested that the Rogue Trader House also has ties to the Inquisition. It should also be noted that the Space Marines remained part of their chapter and did not wear the colors of the Rogue Trader House.

With regards to the original post, the Dark Heresy adventure trilogy involving the Haarlock Rogue Trader lines makes distinctions between the Warrants of Trade issued in the days of the Emperor - sometimes by the Emperor - and the far more limited Warrants of Trade issued in current time.

While I don't let my players have Space Marine detachments on their ships, I do let them use Space Marine gear - specifically vehicles. Imperial Guard and Imperial Navy fighters either fight in space or in an atmosphere. Using Thunderhawks - which can fly around both - just makes more sense to me at least.