With absolutely no plugins enabled (even GP Premium disabled), Back to Top will only appear on the live site with 2+ widgets now. It never appears in Customize.
Then I re-enabled GP Premium and Simple CSS, and now it works as you say it should: 0 footer widgets and it appears, in Customize and in the live render.
Maybe a bad, temporary caching issue? I re-enabled the only other plugin I have (BreezingForms), and it still works properly now.
Disabled/re-enabling plugins fixed it, whatever the culprit.