It is relatively simple to reproduce the issue without even custom recipe: 1) bitbake strace or bitbake gdb. 2) Check the log.do_configure "config.log". 3) See --host being the target rather than e.g. x86_64-linux.
It is my bad. I have to inherit cross, and that is about it: http://www.yoctoproject.org/docs/current/ref-manual/ref-manual.html#cross-development-toolchain-generation