Jeroen Demeyer added the comment:

Sorry for the late answer, but yes: I found this out using an actual 
compilation.  I must admit it was in a bit of an usual situation (32-bit 
userspace on a mixed 32/64-bit mutilib installation), but most other software 
packages have no problems configuring correctly in such a situation.

I can imagine that it's not a trivial change and would require some redesign.

Some more context: this was discovered when building Python as part of Sage, 
see http://trac.sagemath.org/sage_trac/ticket/12725 for the downstream bug 
report.

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