Windows software running in Wine/Proton can bypass the Windows layer and call Linux stuff directly. This is fine; Wine isn't intended to be a security layer by itself. Some of the Proton bits that Valve made to build a bridge between Windows games & the Linux Steam client does this, as well as pretty much every other bit of Wine internals.
Easy Anti-Cheat detects that it's running in Wine and if the game dev enabled Wine support, it downloads a binary that knows how to do that. That version of EAC doesn't run at kernel level, but it does scan your Linux userspace for cheats, or whatever Epic feels like doing today. As with every userland anti-cheat, the company making it can update it more or less anytime you're playing the game and since it's running in the context of the game, it has access to everything the game does. Same thing for most anti-cheat software really.
There are community backports (like Sury's Debian builds) for PHP, including a branch of PHP 5.6 originally released in 2014. Most other notable languages and major packages have something likewise as well, right down to major packages like Drupal 6. It's not always easy, but it's doable and the work is usually either already done or can be paid for.
Weird things that are truly too difficult to support are also often excluded. Eg Spectre/Meltdown fixes were non-trivial and had to be backported to a fairly wide range of things but that only went so far back. Some old systems just never got those fixes and instead have to be ran with a workaround ("don't run untrusted code"). I don't know how things are with the new offering but large complicated packages with lots of moving parts like OpenStack used to be excluded from the full extended support cycle before as well.