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In my understanding, this comes down to LLVM IR code embedding type information for symbols. rl_pending_output is defined as an int. Linking against a function char rl_pending_order() works without lto because it ignores type information, but with lto it's a mismatch and the function is indeed undefined.
Passing ac_cv_lib_readline_rl_pending_input=yes to compilation works around the issue and php cli and fpm compile successfully. Embed SAPI fails, but that's for a different ticket.