gotcha, gotta buy core ships at that point
Yep. If only ship templating would work properly. Might as well wish for design parameterisation or type placement*.
The ability to specify the balance between the various (up-gradable) equipment classes. Example 10% engine, 20% shielding, 5% sensors, 5% life support, 50% beam weapons, 10% armour and the rest 0%.
A placeholder piece of equipment with a class and stats to be placed on a hard point in the design. Example a 'beam class placeholder'. This allows the player to add this piece of equipment to the ship design with specified scale, orientation, animation, and other settings (including something like an order number). The auto designer should then replace this placeholder with the current beam weapon in the game.
Of course this means there should be placeholder pieces for Beam, Kinetic, Missile, Shield, Armor, Point defense, Engine, Sensor, Life support parts and possibly even for the modules like the transport, colonization, and construction modules.
When you then develop (research) a better ship tech the auto designer should upgrade the placeholder piece with the state of the art version of the right class. It should honour the distribution of mass as specified by the parameters. By giving the placeholder pieces an order number he can even determine which ones to use when. For example you could design a ship with 5 missile placeholders, so when the auto designer needs only to place 3 he will know which 3 to use.