This would increase the build limit. Build limits are not based on entire buildings or number of plots, but on Pologons, or triangles and draws, so by doubling up a building (i.e. one in side the other) will increase both triangle/draw, whether you can all or both building or not.
You may have done this, I have a number of times, place a floor on a floor and they look like one? To us its one floor but to the game, its two sets, so twice as many triangles even though as I said above, it only looks like one floor piece.
Figured I'd show some images just in case
In your case though, the build limit is not the main concern, more as to why you are getting double builds???
My First questions are
1) Which console - Playstation or PC
2) Installation way (If PC), Mod manager or Direct
3) ROTC plan - Optimised or Original
4) Plan Design - Random or Designers Choice
Increasing build limit
Hmm, I hear this alot not just here, in many forums, but there is NO sound advice of limit, well when referring to PC anyway.
Consoles are fixed machines, i.e. every PS4, XBox One s or Xbox One X are built the same, a "Fixed Box System" so of course as for one which mainly be the same for all. Sometimes there maybe only slight variations due to mods etc.
PC is a whole new world as they a "Frankenstein Machines" but there is still a limit and this is often missed by the over excitment of bragging about ones system. Yes you might have the lastest 10 million pound system, designed by God himself but what you dont have is a better Fallout 4 Game Engine, just remember, the hard you push something bigger, the bigger the break, the more the damage, then everything explodes in a ball of fire and we all burn........................ sorry got a bit carried away, I do like a bit of fire.
Anyway for PC users, if you get issues and you used a mod manager,
1) uninstall it and do a direct install. Does help in a lot of cases.
2) Check your settings - SS Holotape
3) Blow up your city and start again
4) Check your mods.
5) think about your computer limitations when increasing a build limit
Now I have had issues with build limits well before SS, Fallout 4 is a bug fest even in vanilla, so I have always used a mod to increase the limit, but I never build to it. SS isn't really the issue unless you have a bad install or scripting issues, so you can try things like Fallrim to take a peek at your saves, but try to check as much as possible first, mods, installs and so on.