Alesto wrote:
There is an important I forgot. We need to design a docking interface used by the stations. These should be compatible with Skylark and desirable with all coming freighter types we will have.
The Skylark, being an aerospace craft, has a specific curved geometry around it's cargo hatch. So to create an interface that hermetically seals to it, plus other freighter designs, something special will be needed. What should work best is for the Skylark to extend a level, square docking interface of its own to meet the station's.
As for the station's interface, it would need to be designed around all of the small or specialized freighters that don't use large exterior containers. The challenge here is only the Skylark has been modeled, so we don't know exactly how the interfaces of the other freighters will look yet.
Alesto wrote:
I've taken a look how the interior could be planned. For me it seems that there is not enough room for crew area. Possibly we could move the reactor behind the cargo area. What would you think?
I already did this actually.

There really isn't enough space for it in the middle section. Further, I think we should go back to your original idea that the reactor is not directly accessible by the crew. The technician can manage it from the cockpit with a remote interface, but for him to go to the reactor room he'd have to travel through the cargo bay, which would be so packed full of cargo there would be no room for him to pass through.