Android - Installing magisk with Android 11

Certainly not. It's safe

All that you are doing in this step is to

• Check if your device is recognized in fastboot mode by fastboot devices

• Replace the boot image by the patched boot image on your computer by fastboot flash boot xxx.img.

• fastboot reboot will boot you into OS where you can verify root as next step recommends.

This the normal way of rooting using patched images and will not affect your installed apps. See Magisk official documentation