I would exercise caution with how people read into this comment - a way to interpret this is the that we'll have collaborations with games beyond just the "6 games", so we'll probably get a lot more games than that referenced in TSA that will just be included as mere easter eggs while some like Hotline Miami will obviously get "main billing". That doesn't mean all levels won't be based on actual games. This makes Suda's comment about still wanting more indies to reach out to him make sense.
I'd be kinda shocked if Shovel Knight doesn't get an actual level. But admittedly if all six worlds aren't indie crossovers, I'm expecting a Let It Die world all the more, and I'm still holding hope for that Danganronpa crossover.