Apologies for what may be a naive question; following the XonX build instructions on a fresh 1.3.1 installation does not result in any Xservers being built. Before I get too involved in working out what's going on, I should ask whether this is meant to work in the first place.
The top of the tree at XFree86 CVS does build and work on Darwin x86. There are however a few caveats. First you need to turn off the building of Quartz support since there isn't such a thing on pure Darwin (x86 or otherwise). The cool way to do this is to put a host.def file in xc/config/cf with the line:
#define DarwinQuartzSupport NO
The brute force way to do this is to just manually edit the appropriate line in xc/config/cf/darwin.cf.
There has also been some discussion on the Darwin Development list that the CVS checkout of projects as big as XFree86 have sometimes been corrupted when checking out to a UFS volume. See the archives at http://darwinfo.org for more info.
Assuming you get a clean copy of XFree86 and turn off Quartz support, you should be good to go.
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