Usage of \usepackage{appendixnumberbeamer} as suggested by the documentation can lead to problems, see #365.
Metropolis uses the macro \inserttotalframenumber for calculation of the progress bar length in the templates for progress bar in * (see e.g. beamerouterthememetropolis.dtx:195). Using \insertmainframenumber (see beamer class docu) would solve the issue.
I think its a good idea to get rid of the external package when the beamer class actually already provides a counter that excludes the appendix.
One could also make this configurable I guess, but I don't see why someone would even want to include the appendix pages in the progress bar.
If you agree, I can make a pull request.