Just maintain a config.cache file, either hand-written or obtained by running configure in the emulator or real hardware. I ported ROCK Linux to PowerPC in three days at 16C3 using an iMac G3 for testing and running configure scripts. Most builds were cross builds from x86.
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This assumes your target is also linux or very similar to linux... such that it has all the toolchain, library, shell, etc, infrastructure to be linuxy enough to run autoconf successfully. I have not, primarily, worked on target systems that are sufficiently similar to linux.
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But then you'll have the same issues with a native build, so I personally wouldn't call those problems cross-build problems then.
End of conversation
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