I ran lintian on a non-native package (that is, a package which might
have differences from upstream) which uses native source package
format.

This is in accordance with the Technical Commitee decision
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1007717#384

This reasoning surely applies to lintian too.
In practice with current lintian I see this:

  E: bedstead source: malformed-debian-changelog-version 002.008-2 (for native) [debian/changelog:1]
  W: bedstead source: debian-watch-file-in-native-package [debian/watch]

(The package has a source format of 1.0 native.)

IMO:

 * lintian should determine whether the package is native from the
   version number, rather than the source format.  So it should expect
   a watch file iff the *version* has a revision.

 * lintian should not issue a lint of any severity about native
   source formats with non-native version numbers.

Thanks,
Ian.