For national championships, the Tour can't risk rider (or anyone else involved with the Tour) contact with people outside of a small group. Nationals have too many people involved, including ProConti and Continental Teams, that won't be involved with the Tour. You can have the Nationals, but no one involved with the Tour should participate.
Lombardia doesn't impact the Giro discussion since riders can still ride both. Only the AGR and LBL overlap. None of Bernal, Roglic, Mollema nor Pinot are contenders for those. Maybe Roglic could be but he hasn't shown it.
Of course, Mollema isn't a GT contender. IMHO neither is Pinot. Since finishing on the Tour podium 6 years ago (8 min behind the winner!), he has more DNFs than finishes in GTs and was only remotely involved in the GC of one (2017 Giro).