I know, the rotate thingys are just too much work, and often doesnt work out as you expect.
I would want a simple mouse-wheel scroll while having a part in my "hand" to rotate it around, instead of spending nearly 5 minutes on a single hardpoint trying to get it to face the right direction

How about just adding a "Summetry" checkbox when adding things to the ships. If you add one thing on a hardpoint, you'll get the the same thing mirrored on the reverse hardpoint. This would be easier than having to manually select and rotate and place a differently aligned object.

Also, I haven't even used this feature yet, I would like to, but there are just way too many upgrades in the techtree for it to be practical in the game. I would have preferred it if they'd kept it to design only, with no visible ability add-ons, so that you'd be able to choose from a larger pool of custom and prefabricated designs that'd fit the stats of the ships. In my games I tend to use a nomenclature even to keep track on the different types because there are just so many, with governing stats for descriptions. My five cents.

Brad has mentioned that they will be making future updates to how the ship builder works, so as to make it more intuitive and robust. But I would think that is a major project so you may need to wait a few months for something to come together on that.