Turns out this menu option is somehow linked to the "JIRA Users" Global Permission.
I had deleted the "users" group, intending to migrate to project roles entirely, but you can't add the "administrator" group to the "JIRA Users" Global Permission. I recreated the "users" group and added it back to the "JIRA Users" Global Permission, and the menu option came back.
Hope that helps someone in the future!
If you have administrator rights, make sure that you have the "Create Shared Objects" global permission. Also make sure you are configuring your own issue filter - not someone elses. If you have these, there should be no reason you can't configure columns. Contact support if you're seeing otherwise.
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