Welp, I took off my hood deflector and guess what? No flutter.
It seems that the way the hood deflector juts out at the tip of the hood creates a lifting action. No hood deflector, problem solved.
Current: 2016 Toyota Highlander XLE in Predawn Gray Mica with Ash leather
Former: 2013 Nissan Pathfinder SL Premium in Dark Slate with Charcoal leather
2010 Subaru Legacy 2.5i Premium in Venetian Red Pearl with Black cloth interior