Can you augment your ship. ie, you have a cruiser and come into some cash (and connections) so head onm over to the local Mechanicus facility and fit an Armoured Prow (or other do-hicky). In other words can your ships grow and advance, with upgrades and retrofits. If so would this be a way to get a Battle Cruiser, which is after all a stripped down Battleship or souped up Grand Cruiser?

The book itself states that the reason you are not allowed to get a hull any bigger then a Cruiser is because logically no Rogue Trader would ever have access to them. As there only a handful of Warrants of Trade that divine.

As for upgrades, yes. The book contains a large amount of Components in order to stylize the ship to your liking, and leaves it open for GM's to tailor their own components for some more flavor.