This is pretty normal, if you want faster compilation try QMK WSL. It's a little more complex to setup but works well.

Is this expected because MSYS is slow, or is there a problem in the firmware?

Expected and partially being tracked in qmk/qmk_distro_msys#23

Is WSL faster? And can you flash with WSL2 now or do I have to use QMK toolbox?

WSL is much faster (it's essentially a Linux VM), as long as you keep the qmk_firmware repo inside the WSL filesystem: microsoft/WSL#4197

You can also use Docker to compile, and flash with teensy_loader_cli.exe (depending on your keyboard).

I have example with that. It also includes a vscode .devcontainer environment, so if you use VSCode you can also use C++ environment with all the goodies. https://github.com/Ciantic/CianticQmkKeymap

Decided to setup QMK in WSL and yeah it is basically as fast as my linux boot. Only annoyance is having to flash with toolbox. I got VIA working though I can use that to fiddle around.

You should be able to flash most things using the QMK WSL distro I linked earlier.

Also, make sure that you're using WSL version 2, if your system supports it. v1 is okay, as it is faster than MSYS. However, version 2 is a LOT faster.

Since while ago, savvy users have started using command like this. @xsrvmy
make preonic/rev3:default:flash DFU_UTIL=/mnt/c/QMK_MSYS/mingw64/bin/dfu-util.exe
within arbitrary WSL2 environment + QMK_MSYS or QMK-Toolbox installed to the host environment.

#13431 (comment)

Since while ago, savvy users have started using command like this. @xsrvmy
make preonic/rev3:default:flash DFU_UTIL=/mnt/c/QMK_MSYS/mingw64/bin/dfu-util.exe
within arbitrary WSL2 environment + QMK_MSYS or QMK-Toolbox installed to the host environment.

#13431 (comment)

That's ... effectively what QMK WSL is doing. 😆

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