Oh wow, I did not realize this was the case!
There wasn't any sorting applied to the primary base, the buildings simply appeared in the order of their creation, which I agree can be confusing!
Unfortunately, I can't sort buildings alphabetically, as the game is theoretically designed for many languages and this particular sorting aspect is performed by the server (and the server doesn't know which language your device is using currently). However, I've changed the sorting to be the same across all bases (using our internal identifiers for each building), please let me know if that's better!