Note that autotools handles all that (referencing also your link in another child comment) for you with no extra work. Writing a autoconf script for a native architecture means your project should compile for a cross arch.

It is for that reason I much prefer autotools, especially at the distribution level where you really don't want to be patching things. CMake can work, but I have had to do more patching for CMake build systems than I have had to for autotools; on that basis I consider autotools "better", at least for our use case.