Flatpak is simply a sandboxed application, similar to a Docker container. Its better to have natively installed applications over sandboxed if you are seeking the highest level of performance.
You have essentially made all your games run within a sandboxed instance which has a limited set of binaries that emulate another mini OS within your primary OS.
If you haven't seen any performance issues, then keep on doing what you're doing, the software is very well made compared to Ubuntu Snap and likely has similar driver performance as close as possible to bare-metal