What if we have an overall "sort by usage" toggle? So we can sort by usage as a default, but if people want to customise it they can do so by dragging/reordering lenses in the settings interface—which will then be mirrored by what shows up on the main page!
That way there's no inconsistency in the order. Also, most people will get their auto-sorting, but those who are particular about it can go manual.
(To make the UX smoother, we could say that when someone attempts to drag one of the lenses to rearrange, it automatically turns the toggle off, and they can manually turn it on again to revert to automatic sorting).