I would redefine the problem - because beyond earth or our solar system most of Superman's invulnerability is lost outside the influence of our red sun, so: It is difficult to design a Superman game set on earth with the main character being Superman playing well and selling well while dealing with Earth level threats IMO - which are essential threats for big sales numbers because the subset of Superman/DC fans familiar with the bigger threats to Superman in the wider DC universe is tiny compared to the target market including myself largely being in the dark.
My opinion - and it has been for decades - is that the game should be about his real vulnerabilities - not in his alter ego Superman but as the refuge alien living as a regular human and his true persona - Clark.
You could completely mitigate the flying by using a linear old school Rocketeer game mechanic where fast travel is triggered on launch flying to avoid any need for UE5 matrix demo, MS flight Sim or No Man's Sky implementation requirements that would ultimately feel baren, and do that while still having game mechanics with localized flight that could bullet time his "faster than a Speeding bullet" (+300m/s) in MGS1 top down puzzles maze stealth puzzles mostly as Clark.
If a human can walk about <0.5m/s casually, and run at <10m/s straight line - pro footballer/athlete speed - or <2m/s with directional changes , in bullet time Clark's walk speed could be at <15m/s, and running with directional change at <60m/s giving plenty of scope for security systems, etc to stop the gamer succeeding to save hostages, etc especially if solving solutions in two opposite locations or more in the time limits while protecting Clark's secret identity, star fox/space harrier styled wide narrow gaming could also be used for less local flying game challenges.
It is very doable in design, but easier as a linkage of wide narrow sub game sections styles in the way how games were made in the 80/90s - but with today's advances in tech