It is more complicated than that. They would have to reprogram the Settlement rewards themselves, because presently you cannot get a main building unless you start there from scratch. So they would have to figure out how to program the ability to procure a replacement by somehow resetting the Settlement rewards without a loophole allowing more than one main building. The programming restriction isn't on whether you have one or not, the restriction is in the Settlement rewards. This isn't simple (like them just replacing them), so quit trying to make it so.
Sure, they could have been saved, but once power creep set in there was no reason to assume they would get the massive upgrade needed to make them relevant again. GBs can't be stored, but you always have the ability to replace them. Always. CS buildings=Can't replace. GBs=Can replace. Simple as that.