We nowadays record NMUs via X-CRAN-NMUlist entries in the PACKAGES.in
CRAN repository db, e.g.

  Package: gridExtra
  X-CRAN-NMUlist: 2.3.1

When putting an NMU for a package on CRAN, check whether the current
version x.y.z for the package is in its X-CRAN-NMUlist.  If so, change
the version to x.y.(z+1); otherwise, change to x.y.z.1.

In both cases, add the new version to the X-CRAN-NMUlist of the package.