Are Sanctums two-player co-op?

In practice this means you cannot walk into one alone. Certain Sanctum puzzle dungeons enforce a minimum party size of two, so the instance will not open for a solo player no matter how strong your team is. Line up a partner before you travel out to one.

It is also not a case of bringing a friend along as a passenger. The puzzles are built to be solved by both participants using their Aniimo on the tasks together, which means the second player needs their own creatures and needs to be doing something with them. These are instanced dungeons and puzzles, sealed off from the open world, so what happens inside is between the two of you.

How this differs from the rest of the co-op

Most multiplayer in Aniimo is optional company. Your main world is a private instance and you can invite friends into it to explore and catch creatures alongside you, but you are never forced to. Boss encounters work the same way: world bosses and Alpha Aniimo bosses can be fought cooperatively, and a group makes them easier rather than possible. Farming is the same bargain, where tilling soil or helping out on another player's farm pays you a portion of that farm's harvest.

Sanctums are the exception. They are the part of the game where a second player is a requirement rather than a convenience, so they are worth planning around if you tend to play alone.

Not settled: Two is the stated minimum for those Sanctum dungeons rather than a stated cap, and whether a larger group can enter one is not settled.