Not only that, why is there such a huge difference between ClearLinux and Ubuntu/OpenSUSE?

Most video encoding, I assume, happens on linux machines these days. If switching a distro can result in such drastic improvements, it can result in massive savings for the big players, like Youtube and Twitch.

If it's related to the thread scheduler yes. If it's related to compiler flags then the big sites probably have their own optimized builds of the encoders already.

Hard question to answer without knowing what compiler was used to build the binary, what version of the code was built, what build settings were used, etc. Video and audio encoding tools are the perfect example of software that will have wildly different performance characteristics depending on compiler optimizations; making comparisons between different operating systems a really unscientific process unless you use the same toolchain across all of them.

Are you reading the graph wrong? It says "Seconds, Less is Better".

Yes. Windows 10 took 6.27 seconds, with the exception of Clearlinux all the Linuxes took 8+ seconds.