Even if the limit becomes global, the issue remains for all existing buildings, all future buildings, and this still allows dog kennels to be made to train dogs faster. (I do believe that training dogs faster is not that big of a deal and the existing building's limits being bypassed is not that strong, but it makes it harder to balance buildings in the future.)
The best solution I can think of is to make limited buildings get destroyed when captured by an enemy or Gaia as they are all civilization exclusive and it could be argued in a real war they would be burned down.
Another way to solve it would be to make the buildings not decay to Gaia that are limited, but that still leaves the exploit of a teammate not on your team being able to capture them and allow you to make more.
I believe that bypassing the spacing limits between buildings using this method is far to inconvenient to be useful and not being able to place towers near other peoples towers would be no fun so I think it should be ignored.