The flatpak has all of the required dependencies included in the file and are sandboxed when you run the program. Typically installing the app via your package manager or storefront would rely on dependencies previously installed on your system or install them during the setup process, and running them on the system will draw those resources from wherever they’re stored. This is why you’ll find flatpaks are typically much larger than the footprint of a traditional program on Linux.
I can’t say for sure but I’d venture a guess that the code for the emulator hasn’t necessarily changed, so they haven’t seen fit to iterate the version number in some time, but the flatpak was rebuilt to include the newer versions of dependencies that interface with your newer hardware. Just a guess though.
Have you tried the flatpak to see if it solves your issue?
You don’t need an sdk to set up flathub.
I don’t use Ubuntu but reviewing the commands on the flatpak website they seem pretty straightforward.
https://flatpak.org/setup/Ubuntu
From there you should be able to install Kega from the Kega listing by clicking the install button.
https://flathub.org/apps/com.carpeludum.KegaFusion