This popup was recently introduced in PR-2174.
I don't know exactly why, but voyager prompting me that I'm about to lose my progress was sort of strange to me in the context of scrolling on lemmy.
I understand why someone wants such a feature, but IMO this should be turned off by default and available as an option.
I have gestures disabled but I get to the communities list by pressing back.
Even disabling all swipes you can still go to the list swiping the left margin to the right.
Over all it is annoying but not much of a problem because I browse hiding the posts I've already seen so I'm never too far from the top.