Oh, I probably should have noted config.log seems to be complaining
about this:

gcc version 3.3.3 (NetBSD nb3 20040520)
configure:2385: $? = 0
configure:2387: cc -V </dev/null >&5
gcc: couldn't run
`/usr/bin/i386--netbsdelf-gcc--I/usr/pkgsrc/textproc/libxml2/work/.buildlink/include':
No such file or directory

Which indeed there isn't.  And later:

configure:2416: cc -O2
-DXML_SGML_DEFAULT_CATALOG=\"\\\"/usr/pkg/etc/sgml/catalog\\\"\"
-DXML_XML_DEFAULT_CATALOG=\"\\\"/usr/pkg/etc/xml/catalog\\\"\"
-I/usr/include -I/usr/pkg/include   -I/usr/include -I/usr/pkg/include
-L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.c
>&5
<command line>:4:27: missing terminating " character
<command line>:5:26: missing terminating " character