If they did let WvA contest the sprints in stage 1 and 3, he may have led the points competition by now. Two times 5th would have been enough. Maybe on stage 1 he could have done even more.
There is absolutely no doubt Van Aert can take green in Paris, if the team makes it a priority.
But, for a team that has never won the Tour, it might be wise to actually try and win the Tour first, and then worry about green next year