Keep in mind that you can not put components in SMALL cargo holds at all, only standard holds.
On the general subject, I use civilian shipping for a lot of stuff, so I keep track of the exceptions.
You can't ship Ground Force Training Facilities, components, PDC parts, tracking stations (I think, not 100% sure), salvaged tech points through the civilians. And you can't ship fuel directly either, but you can let the civilians build fuel harvesters, merge them into a task group, suck the fuel out of them, and destroy them so you can scrap their wrecks.
So I plan my commercial ship building around what I can not do with civilians.