May I ask why the choice of the *.ntp.~<n>~ format?

• blender uses .blend1 .blend2, etc. By default, these files should not be opened by blender without removing manually the number at the end.
• On Unix systems, a ~ at the end indicates a backup, and most file browsers understand it that way. Even blender users are asking for this, see https://blenderartists.org/t/hide-backup-blends-with-tilde/1165342 and https://blender.community/c/rightclickselect/Jsdbbc/?sorting=hot for a request to do that
• For numbered backups, it must have a ~ at the end but also a number. The best reference I could find is to use .~{number}~, see here: https://ftp.gnu.org/old-gnu/Manuals/emacs-20.7/html_node/emacs_103.html
• Backup files should never be opened by Natron without having been renamed explicitly, else how do you backup these? This is also how it works in Blender
• I could change the default so that if only 1 backup version is asked (the default), it just adds the tilde instead of .~1~, but then corener cases may be tricky to handle (what happens when saveVersions > 1 but there is a ~file?)

Oh and also GNU utilities cp, mv, ln have the option --backup=numbered which use that same naming convention.
See http://www.jpeek.com/articles/linuxmag/2005-08/

May I ask why the choice of the *.ntp. format?

blender uses .blend1 .blend2, etc. By default, these files should not be opened by blender without removing manually the number at the end.
...

Oh and also GNU utilities cp, mv, ln have the option --backup=numbered which use that same naming convention. See http://www.jpeek.com/articles/linuxmag/2005-08/

Fair enough LGTM then