It's not more egregious. There is no deduction for landing on a different foot and she displayed decent control of the landing and didn't heavily slam her other foot into the ice, which is what happens on the most
egregious double-footed landings.
Her 3F had no edge issue, there was a very clear 3-turn in and no lean to the outside. An "inside edge" shouldn't be the strict requirement for a Flip in the first place; doing that jump from a straight edge has historically been considered correct and should continue to be the way the jump is assessed.
The 3Loop was totally fine. You're clearly not measuring the actual rotation. This is her landing:
She takes off with her skate facing the board behind her, or slightly past it. The angle of this landing is unquestionably far enough around compared to that takeoff angle.
Alysa is the one who has actual rotation issues and should be getting lower GOE for her huge pre-rotations on the Lutz and Toeloop. Nakai's Flip and Loop were totally normal jumps. Any system or judge that tries to hammer those jumps is a bad system/judge. Bullshit like this that operates contrary to reality has been negatively impacting the sport for far too long.
This is a dumb thing in the scoring system. Doing a 1T is a bad and doesn't impress anyone. It's visually always a mistake within a program. Whereas a solo jump does not interrupt the flow.
It's another reason why the system should give bonuses for jump combos, and not have the REP deduction. If you leave out a required combo, you're already losing a significant amount of points.