If I'm not mistaken it's all about system, stock starbase is used on several system in KM and in at least one system in stock BC - namely in Starbase 12 system, editing that system script to load different/replacement station should do it but beware, it might also cause some additional problems with the system itself (unable to dock, crashes to desktop, etc. ... not to mention mission scripts ...)
I think it would be easier to get replacement starbase model, rename it to stock model's name and then overwrite it, do the same to hardpoint and you should have it done, still you might get problems during SP missions (ships positions and docking)