Does Freemasonry recognize the Church of Scientology as a religion?

It doesn't matter. Scientology fits the definition of a religion and opinions are irrelevant to that degree. So, It doesn't matter what any other religion or organization thinks. Freemasonry is not a religion, BTW.

Freemasonry does not engage in the practice of "recognizing" or not the legitimacy of any person's chosen religious beliefs or of any religious organization. So Masonry has no opinion on the matter.

When becoming a Freemason, no one will ask your religion. What will be asked is the "short" question, "Do you believe in a Supreme Being?" or the "long" question, "Do you believe in, and put your faith and trust in one supreme and supernatural Creator of all the Heavens and Earth?" (varies a bit place to place, but that's the jist).

We are a Fraternity and take no stand in 'recognizing' any organization or church or corporation. Whether individual members do or do not, as a whole Freemasonry takes no position whatsoever.

We are a Fraternity.

There is Freedom of Religion for all.