We claim the privilege of worshiping Almighty God according to the dictates of our own conscience, and allow all men the same privilege, let them worship how, where, or what they may.

An after thought? A claim to appease church critics?

Because, mormons certainly don't follow it. Every member a missionary. Reactivate inactive members to the point of harassment. Baptisms for the dead. Excommunicate members that join other churches.

Does quoting the 11th article of faith to mormons have any effect?

They were written as part of a letter to a newspaper editor, the whole set are a PR gesture.