Line a 9-inch square cake pan with parchment, leaving a 2-inch overhang on two opposite sides.
In a large bowl, combine cereal, cranberries, pepitas and flax seeds.
In a small saucepan over medium-low heat, combine nut butter, honey, cinnamon and kosher salt; cook just until completely smooth (do not bring to a simmer), 1–2 minutes. Off heat, stir in vanilla. Pour nut butter mixture over cereal and gently, but thoroughly, mix until cereal is completely coated.
Transfer cereal mixture to prepared pan and press firmly into an even layer using flat bottom of a measuring cup, bowl or glass. Sprinkle with flaky sea salt, if using. Cover and chill at least 1 hour, or preferably 4 hours.
Lift bar out of pan using parchment overhang. Slice into 10 even cereal bars.
Store cereal bars between layers of parchment or waxed paper in an airtight container (or individually wrapped in plastic wrap) in the refrigerator.