By definition it should obvious the million-user server is a popular feature since it has a million user.

Not necessarily, if Discord has more than 200 million Daily Active Users, and there are a few million-user servers. Those million-user servers could mostly be made up of the same million users (or only a small percentage still actively engage but they never left because there's no disincentive to leave servers instead of just muting them) meaning it's used by less than 1/200th of the total users of Discord.

Realistically, that's probably not the case, but it's impossible to know the true popularity without more statistics.

obligatory citation: "Nobody goes there anymore; it's too crowded." —Yogi Berra, MLB HOF catcher & manager