Part of the problem is that we are ignoring some fluff and not others; like I mentioned earlier, it is pretty rare to have as many SM in the field (other than fleet based chapters) as we play in games; a 1500pt fleet could have two battlebarges alongside a pair of strike cruisers and a squadron of escorts. The odds of the chapter pouring that many resources into one battle...it would have to be for their survival to warrant risking that many marines. In space, all it takes is one lucky shot to wipe out a third of the chapter after all. Other than the horus heresy and the battle for maccrage, the only references I have seen to such massive fleet engagements are the Iron Hands novel, the redemptive crusade in the new Chaos Codex and the Badab war.
It is fair to assume that if the chapter is fielding 75% of its vessels that it will have brought a lot of marines to woop ass...at least, that's the way I see it.
To add to specific chapters abilities, there is mention in the Deliverance Lost Horus Heresy novel that Corvus/Corax has had all the Raven Guard vessels modified with improved energy baffles and cloaking fields, allowing it to pass virtually invisible as long as the shields and other high energy systems were down. Later, if we were so inclined, the RG could buy mimic engines of sorts, to represent their silent approach.
In Fulgrim (Horus Heresy), there is reference to the Iron Hands vessels having lots of access to castellan void shields (bonus if your ship has them in RT), which basically allows some of their shields to pop back up sometimes after an overload. Could have upgrade that allows shields an save of sorts, 5 or 6+.
In Hunt for Valadorious (SM Battle Book), the White Scars have a ship that basically has evasive jets like the chart upgrade.
In Salamanders trilogy (tome of Fire 1-3), the salamanders have masterfully crafted hulls which are more resilient than other ships equivalents. No real way to implement this, but...
I could go on and on, but I think we can all agree that this can be a separate compendium for expediency's sake.