By running your applications in Flatpaks, you're isolating them from the rest of your system. Essentially, Flatpaks save you from ruining your system because you installed 10 different copies of the wrong graphics drivers, while following random guides on the internet.

Running games in flatpaks ensures you're using the latest drivers, so you dont really have to worry about it. It makes things SO much easier to manage from a linux gaming perspective.

That said, Flatpaks introduce a different kind of complexity to your system and there might be a bit of a learning curve before you feel confident troubleshooting any issues that come up, especially if you have no experience working in containerized environments.

Personally, I'm coming up on a year of daily gaming in Flatpaks and I've never had any issues.