As long as it’s kosher, it’s kosher, so of course we can be yotze. The reason we prefer using a Lubavitch mikva is because of the hiddurim involved which basically make it that a woman toivels within the bor itself. This is accomplished by it being built bor Al gabei bor, and the bottom one is cold, and 80 seah, so no chashash of the original 40 being whittled to less than the shiur. Also the water filled in on top is hot, while the bottom is cold, so that avoids mixing.
This avoids many problematic issues involved with other kosher mikvaos such as the one that’s next to the bor with a hole in between, kept apart with a plug- let’s say the mikva lady forgets to remove the plug CVS, then the woman didn’t toivel in a mikvah because it wasn’t connected to the bor… There are other issues with the other prototypes, and this model was developed to avoid all issues