So can this be resolved? When I would enable Settings > Align cursor on
frames I don't have this issue. I would say, if Cinerella causes these kind
of out-of-sync behavior, should we even have enable option (by default) not
to edit at frame level?

The default setting is "Align cursor on frames" which is a good default to prevent confusion for the majority of users who edit Video and who would never even be aware of this aligned setting.

"Align to samples" is used when editing just audio and it makes sense to do that since there are no frames.