Steve,
I think alot of this ends up being 6 of one and half a dozen of the other. Indeed most slipways in a shipyard are geared to a certain size of ship and if possible depending on the amount of ships being generated geared towards a specific class. This increases effeciency and reduces cost of course and like your last post would not affect it too much if there were minor changes to an existing design.
Slipways are generally however grouped as many together as there can be because having them in one shipyard also increases the effciency by allowing mutual storage and easier construction on similar components (even carriers, cruisers, and subs have similar components). This effciency is usually increase by the number of slipways you have (i.e. the more ships you are building at once in the same area be they different or not the cheaper it is per ship). How much of a difference this makes and how easy it would be to program either way I know not.
This concept is also complicated by the way you have designed Aurora. In comparison to Starfire there are far, far fewer ships being produced. For the most part maybe 5 to 8 ships of any given design (I think the max I saw was 20 to 25) seem to be produced before technology has moved on to the point where a new design is ready to be made. It is the problem most shipyards are facing today, they really have no time to learn how to produce a particular class more effciently because by the time they have learned a new class or a new phase is being produced or too few ships of that class are going to be made in the first place. The Liberty ship in comparison, which had some 2700 ships produced, was able to make the transition from 240 day construciton to 42 days because of how many they had to learn from.
So... if your looking for realistic I don't know how much a shipyard could gear itself to a particular class of ship when it might only produce a few of each of that class. Now I can see a shipyard gearing itself to a particular type of ship (ie freighter, carrier, missle ship, beam ship) and only be limited to the size of whatever slipway it currently has. A sub is a sub even it is a SSBN or SSN it has simlar needs and overall characteristics, same as a carrier or surface ship.
It's a complicated problem, guess I will have to see how it games out in testing, but I thought I'd toss my 2 cents in.
Also I was curious. How does this affect refits?