To suppress the warning and avoid false-positive "pending changes," you can add this line to your DbContext configuration:

protected override void OnConfiguring(DbContextOptionsBuilder optionsBuilder)
{
    optionsBuilder
        .UseNpgsql("YourConnectionStringHere")
        .ConfigureWarnings(warnings => 
            warnings.Ignore(RelationalEventId.PendingModelChangesWarning));
}

This line 
.ConfigureWarnings(warnings => 
    warnings.Ignore(RelationalEventId.PendingModelChangesWarning));

tells EF Core to ignore the warning about pending model changes, allowing Update-Database to run without requiring a redundant migration.