As long as there isn't a ton of repetition during subsequent story playthroughs, is this really an issue? You can go to Venom from Bolse and end the game there if you want, or you can start it up again and play harder levels to get there from Area 6. It's not as if it's a massive time investment to go through the storyline to begin with.
The repetition is only a part of it; and really it's not a big part at all. The main reason why I personally don't like the 'replay to get new levels' style is because it devalues said levels. Not because it makes them inherently worse, but because it makes them disconnected from your own 'holistic' experience with the game. They're things you have to go out of your way to do afterwards purely for the sake of it, and that is always going to place them as 'secondary' to the set of levels you happened to get your first time around.
It's a similar problem that many 'narrative-choice' games face, where most players will simply never feel as excited for, say, doing an "evil playthrough," of Mass Effect compared to their first one where they did what they wanted. They might want to, and it's definitely cool that it's there, but they probably won't, and if they do they almost definitely won't care as much. Except, of course, Star Fox games 40 hour RPGs with massive narratives and tons of stuff to do. So, unlike with Mass Effect and its ilk, the moment where you go from "first, exciting playthrough," to "second playthrough you do to 'see the rest'" comes at the 2 hour mark instead of the 40 hour mark.
It also inherently limits what kind of game a 'Star Fox' game can be. If your game is a 2 hour arcadey title meant to be played 4 times over, then you can't do satisfying long-term progression, or an in-depth 'complete' story, or even add much more content lest the game get 'too long' to replay. You can essentially
only make Star Fox 64, but with newer 'stuff.' Which is fine, but not exactly befitting of where gaming is at right now in my eyes.
...that's the idea though? you replay star fox to take the different routes. it's part of the fun
For some it is, definitely. But for many, I think it's a hindrance more than a help, and I've explained some of the reasons why before. That and Star Fox Zero already got rid of the whole "replay the whole game to get to a point," system, so Nintendo themselves clearly agrees with me in some way.