If you flash a stock vbmeta but a modified boot image, the hashes won't match, leading to an immediate boot failure. Magisk's internal patching ensures the boot image "authorizes" its own modifications.
Magisk automatically detects if your device requires specific flags like AVB_VBMETA_IMAGE_FLAGS_VERIFICATION_DISABLED (flag 0x02) and applies them directly into the patched image.
When you use the Magisk app to "Select and Patch a File," it doesn't just inject root; it intelligently modifies the boot image's header to handle AVB.