OK, that is a fairly unique issue AFAIC. What you show there is the old URT (Unified Rear Triangle) suspension, that did often move the BB with respect to saddle height. It was an option early in the development of MTB suspension, that is all but missing in the modern MTB full suspension world. I can’t even think of a bike that has been built upon that design in the last decade or longer.
You are correct, that it can have an impact on setup, but it depends on the specifics of the URT design. Some actually didn’t have much BB shift WRT saddle height. I chose to ignore that possibility since this suspension design is VERY uncommon these days. If the OP happens to have one (via a very old model), then the concern is valid. But I would put $10 on the fact that he has a more modern bike without a URT suspension.
Not to mention that the OP has not even clarified the details of their MTB. Could be a hard tail for all we know. As above, many missing details here.