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.

Time in terms of setting everything up or learning how to use it? Because I can tell you that both are relatively easy. The installation is super easy, no harder than an ordinary Windows setup. The Steam Deck by default uses a desktop environment called KDE, as a Windows user, you should feel right at home. I'd say it's very intuitive to use and easy to learn. As Bazzite tries to mimic the Steam Deck experience as closely as possible, it uses the exact same stuff. Maybe check out this video.