HDF has GSV coverage from September 2020.
That's recent.
How to deal with it - own system(s)?
Seems sensible given the different sign colours - so the Lille Metropole ones would be frahdf
m59, with the Nord department roads frahdf
d59.
Lyon Metropole is it's own department (69M), but you can easily just have it as fraaram69 with Rhone (formerly 69, now 69D) as fraarad69. Métropole d'Aix-Marseille-Provence and Métropole du Grand Paris are special metropoles with more powers (but that speciality doesn't seem to be relevant, and Grand Paris seems wholly unconcerned with M roads).
The standard Metropoles are: Bordeaux Métropole, Brest Métropole, Clermont Auvergne Métropole, Dijon Métropole, Grenoble-Alpes Métropole, Métropole européenne de Lille, Metz Métropole, Montpellier Méditerranée Métropole, Métropole du Grand Nancy, Nantes Métropole, Métropole Nice Côte d'Azur, Orléans Métropole, Rennes Métropole, Métropole Rouen Normandie, Saint-Étienne Métropole, Eurométropole de Strasbourg, Métropole Toulon Provence Méditerranée, Toulouse Métropole, Tours Métropole Val de Loire.
Most metropoles don't seem to have replaced D roads within their borders yet, even if they have created some M roads - but some have done the lot (with a very simple change of prefix and sign colour rather than making a new numbering system), and that seems to be the aim (at least for the normal ones).
And as a totally unrelated aside - this is far less of a mess (other than for road numbering) than English local government. Today's post-lockdown 'what is in what tier' document was a messy mish-mash of items: City Regions, Combined Authorities, Metropolitan Counties, Ceremonial Counties, Non-Metropolitan Counties, Unitary Authorities, counties that were abolished 24 years ago (which they got the name of wrong as well), groups of authorities that they decided to lump together that have no formal link, and three districts that were abolished and combined into one last year that were listed separately.