Slonimer, it is NOT TRUE that “most non-Lubavitch shittos hold makes the mikva not kosher”. In fact there are no such shittos. Bor al gabei bor is the most mehudar mikveh design possible, and the claim that it is possul according to *one* shita, the Divrei Chaim, (not “most” shittos) is a brazen lie that certain people once circulated for political reasons. Anyone who bothers to look up the Divrei Chaim inside sees immediately that it’s a lie.
In any case it’s irrelevant to the Baal Hatanya, because in his day there were no rainwater mikvaos at all, and therefore no question about where the best place to put the bor would be. Rainwater mikvaos only started to be built in Europe in the 19th century, which is why there was so much discussion among the poskim of the time about the ideal design for one.