You go into creative, spawn two copies of the base side by side, as close as you can get them to where you'd like them to connect, go inside of each and remove the core. As you are facing them, try to use the number of the left one and then the right one after the mergestructs command. Usually it will work the first time, but occasionally you will have to destroy and respawn one of the bases. After you get the results you want, use the mergestructs command with -ex after it to finalize the merging and then place a core in the result.

how do you take the core out of a blueprint?

Thanks. Take the cores out before merging to get them to stay aligned.

Nice use of the Zero G drop Bases :)