Sorry, didn't read that last paragraph closely enough. If you're using tarballs, then your getting everything that would be in the development package. Now I have to download the PHP tarball and read the configure script...
Here's the applicable section from the configure script
for i in $PHP_LIBXML_DIR /usr/local /usr; do
if test -x "$i/bin/xml2-config"; then
You can see that the script looks in the bin subdirectory of the user supplied libxml2 prefix, then /usr/local, then /usr for xml2-config. Since you don't have a bin subdirectory, it can't find xml2-config.
There's two things you could do at this point. Either create /apps/libxml2-2.6.27/bin and move xml2-config there or edit the PHP configure script to NOT look in the bin subdirectory. This sed will edit the configure script
sed -i 's@/bin/xml2-config@/xml2-config@g' configure
Edit: Which you figured out while I was writing this post.