I know that you must enter the Workshop and construct or manufacture a ship part there, before you can build one.
It can be a tedious task and time consuming task as well, especially if you want to construct multiple Secret Project ships!
I am suggesting a small, but noticeable and important improvement! It will save time and effort!
Leave Workshop system as it is. Only improve the current Secret Project Interface, so that you can click on each ship part, where you can also manufacture it directly.
How would it work or look like?
your selected ship part would be highlighted with some blinking glow, or just outlined with some color
you need to click on the highlighted field again, if you wish to build another one. It is a prevention mechanic, which prevents you that you would build a duplicate
you can only construct one ship part at a time
by clicking on the Manufacture option, you would be able to construct it directly, without any mandatory access to the Workshop beforehand
if you have enough materials to manufacture a Secret Project ship itself, all ship parts will start to glow, including with the Manufacture option (optional)