If x and cmd+w are not actually closing window, this would technically not be a bug, like the following bug report. However, since opening Anytype through menu bar doesn’t reproduce this behaviour, I will not close this report and leave decision to team.
Also, if this logic cancels out the bugness of behaviour, more objects should be opened…
Edit: I didn’t expect opening the application to behave as reopen last tab in chrome, using cmd+shift+t