Ok, so this next idea is an extension of the previous one, where you have four Component types: SY Hub Module, SY Slipway Module, SY Military Capacity Module, and SY Commercial Capacity Module.
We'll pretty much ignore the Hub Module, it may just be a large, expensive, crew intensive module.
We are going to treat the Slipway Modules like Fire Controls, and the Capacity Modules like weapons. So ships with a Hub Module will have an additional tab on their menu that lets you manage which Capacities are attached to which Slipways, as well as manage which Slipways are assigned to which ship classes, and what they are doing, etc. I'd imagine that just like our other UI redundancies much of this could be managed from the Planet Production screen of the Colony they were stationed at as well (if we are going to keep the restriction that construction must happen on colonies).
When you select the Slipway and the Capacities (you can't mix Naval and Commercial Capacities at this point) and click "Assign" or whatever, that slipway starts being configured. This could be a mix of the existing system and the Fire Control system, in that there could be a research item that affects the length and cost of shipyard modifications, and it could also (perhaps) be modified by Crew Grade. A similar procedure would be used to assign Slipways to new classes, as well as releasing capacities from slipways to go back to the pool of Capacities on the ship available to be assigned to Slipways. The length of work may also be based on the scale of the change, just like now assigning five capacities to a slipway for the first time would take longer than adding the fifth capacity to a Slipway that already has four. If Crew Grade affects the length of any of these changes, then building ships and retooling yards should both increase Crew Grade.
This 'Fire Control' method would also allow subsequent customization to Slipways down the line, similar to how you also assign ECM to individual Fire Controls. For example if you go down this road, especially if you want ships with minerals in their cargo bays to construct ships on the move (like Carriers in Homeworld) then you will probably want to move "Shipyard Construction" from a Planetary Governor skill to a Naval Officer skill. Then maybe you could assign a 'Shipyard Overseer' to the Hub Module, and then a separate officer to each slipways, similar to how Regional Governors and Planetary Governors work now.
It also opens you up to more out of the box thinking later. For example you could research modules that do things like "Increase Beam Weapon Construction Speed by 10%", "Increase Engine Construction Speed by 10%", "Increase Construction Speed of Ships under 2000 tons by 15%", then put those on a Shipyard Vessel and assign them to particular slipways.