There is a bug report on it https://gitlab.gnome.org/GNOME/epiphany/-/issues/638 and it seems it will not be changed because the decided not to have folders but instead tags which doesn't really synchronize well because of that.

Only way for me would be to drop browser internal bookmarks but hm, I'm not sure I'm ready for that. And moving to tags ... I tried it back in the day with deli.cio.us and I ended having more tags than bookmarks, it's not for me.