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From the comment by @Youw here.
Yeap, this is the reason:
For libusb project, we usually recommend using pkg-config to find libusb.h and not to use libusb-1.0/libusb.h in any case.
https://github.com/avrdudes/avrdude/blob/main/src/avrftdi_private.h
It is not enough to install pkg-config. One must explicitly use it to find a package.
The propper way would be to remove things like find_library(HAVE_LIBUSB_1_0 ...)
and similar nonsense with a propper use of cmake/pkg-config, e.g. in a similar way like HIDAPI does it.