I have a question along the same line.
The rules arent entirely clear about this, can capital ships fit inside Stations if they are large enough? What about capitals inside capitals? I do believe I heard somewhere that stations cannot go inside capital ships.
Im guessing that docking ports are supposed to allow for capital to capital or capital to station transfer, but I have no idea if that is current or a future implementation.
You can dock Bayo into MTC for example, so yeah cap in cap is possible. I managed to get station inside a station too, but dont try it too, Zhao wont be happy about getting out again. Now I wonder if you really need docking bay from stations, like BFF could hold LSC for example, if you dont need docking bay.