Well of course they're rare in the Imperium, but so are space battles in general. It is quite true that, in the grand scheme of things, space marine chapters positioned and sized in such a way that they would be assisting Imperial Navy fleets in battle are a rare sight. But compared to some of the other things in Battlefleet Gothic that we see on the tabletop without batting an eye, these chapters and situations are downright
common. One example? Venerable battle barges.
Many Space Marines have no access to battle barges at all. Even the largest, longest lived, and most powerful chapters have less than a handful. Battle barges so old and powerful that they predate the formation of the chapter system and are still worth using in battle are
beyond rare, as likely to be seen in an imperial space battle as an underhive ganger is to come face-to-face with an Eldar farseer. Compared to this, a Space Marine chapter lending a strike cruiser or two in a border engagement is practically commonplace.
In BFG we deal pretty much exclusively in rare events of the Warhammer 40,000 universe. Aside from named vessels like the Planet Killer, almost any fleet or scenario in BFG can be assumed to be something we can reasonably expect to see somewhere at some point; hardly in need of special justification.
Of course, I'm responding pretty doggedly about a non-issue, mainly because I think it's a fun discussion. I fully agree with you Horizon that he should have a good story behind it. It's always good to have fluff behind your fleet, the more in-depth the better! And stories like this, where they're on the 'frontiers' of the Imperium, are my particular favorite for BFG, they really bring out the 'age of sail IN SPACE' vibe that BFG is so good at evoking. I'd love to hear any other fluff you might come up with about your fleet Pembo!