Hi
Many things can be taken in account
As @Lynx3d said, various driver issues, differences in Krita configuration, anti-virus/malware protection products constantly running in the background…
But also the OS
I don’t want to troll and I really don’t care about Windows product..
The only thing I would say on it (even if i can say more as I daily work with 40-60 windows servers at the office) is, Windows use an Hybrid kernel architecture as Linux use a Monolithic kernel architecture.
I won’t tell you which type of kernel is better or not, I’m not good enough for that, but I will just say that different method to use the same hardware won’t give the same results 
Also if you install different Linux distro on the same computer, especially on low-spec computer, you could be able to see some differences.
All Linux distro are based on the same kernel (exception: version of kernel might change )
But there’s not one Linux, but many many Linux distro: a Linux is like a LégoTM, you choose block to build something
And how the distro is build, which component are installed or not, can have an impact on performances: - background task running
- version of software
- the choosen windows manager
- the choosen desktop environment (Gnome, KDE, Xfce, Lxde, …)
- the choosen hard-disk format file system (most of Linux distro might use ext4, but…)
- event logging level
- …
For example, on low-spec computer (low CPU/few memory) use of a distro with a light desktop environment like Xfce or Lxde is recommended instead of using Gnome or KDE
The less the OS need CPU/Memory, the more you have CPU/Memory to run your software
Edit: I forgot
Compiler used to build Krita can have an impact too
Same source code don’t mean same compiled binaries.
On Linux there’s a difference in performance if you use GCC 8, GCC 9, GCC 10, GCC 11
Compiler on windows is not the same than compiler on Linux.. it could also make a difference
Grum999