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I'd prefer e_flags bit. No idea why you want to implement this in crt1.o, I'd just do this in elf_machine_matches_host and in kernel's ELF loader.
For some examples see e.g. sparc, which doesn't use e_flags bit, but has a special EM_ code EM_SPARC32PLUS. The advantage of e_flags is that it can be easily merged during linking from multiple input objects (if any of the input objects has the bit set, set it in the output), and can be cheaply tested by the kernel.
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