I understand this does not work together with Navigation popups.
But before, if you enabled both, Navigation popups will simply override Reference Tooltips. But currently, if you leave Reference Tooltips on (with default setting, "Click") and then enable Navigation popup, it causes a bug that, if you want to jump to the reference by clicking the reference number, you have to CLICK TWICE.
This doesn't happen a few months ago. So I mark it as a regression bug.