It's a niche situation. SFML can be modified by whoever wants to maintain the flatpak package, but we generally don't build in "features" to make it more compatible with some niche package manager, especially when it's about disabling functionality.
If there's a better alternative to udev, then making a proposal to adapt would probably be looked at.
FYI: Even the Debian packages are built with slight modifications to accommodate their quirky setup.