I really appreciate the book references, but consider this:
Your citation mentions: "Her foredeck is so large that it can dock a dozen large cruisers" or as another source mentions "its foredeck can dock a dozen Imperial Navy Cruisers around its circumference".
While I was also basing my approximation off of a 5-6km cruiser, these descriptions are unclear if it was nose-to-nose or side-to-side. Imperium ships are longbois, so a 5km long ship may only be 1km wide. This also tells me nothing about how far they are spaced, but I would not assume you'd want to pack them any closer than 1 km together since many cruisers have odd protrusions you don't want hitting eachother. This uncertainty leads to my approximation of 20-70km (or greater depending on spacing) around the docking area.
Also, the 12 cruisers do not dock around the circumference as a whole, but around the "foredeck". This will be a much smaller circumference than the entire base-ship which puts it on a very different scale than a Ramillies. The cover of the book "Phalanx" depicts it as having 4 arms (one of which is presumably the foredeck), that are each ~1/4 of the over-all diameter of the vessel, and have a circumference that is ~1.5x greater than their length. This makes the diameter ~ 2.67 times the foredeck circumference so that puts us at ~53-187 (or greater) km across.
Last point is the ambiguity in the definition of a "moon" vs a "satellite" planets such a saturn have countless satellites that not considered moons. Generally moons are considered satellites which achieve their own hydrostatic equilibrium (or at very least an ellipsoid shape). This requires a diameter of at least 400km.
Even if you consider non-elliptical satellites to be moons, the large end of moons is still over 5000km within our solar system, meaning without further information, the author could still easily be referring to anything less than 1000km as "small".
So, yes, I know a lot of this suggests a much bigger scaled that you would expect, even in warhammer, but this is also the biggest surviving ship created by the million worlds of mankind over the course of many millia. It is by definition a ridiculous outlier just like the death star is an outlier in star wars.