Well I've made some progress in understanding the problem. Here's what I did.
I started over fresh with PHP 5.3.
I did a bmake and verified that it compiled.
I added the directive --with-axps2=/usr/pkg/bin/apxs

I ran bmake and got a number of errors related to .h files not being found.
I copied and pasted the attempted command into a file.
I ran the file as a script and it compiled????????

This is a very clear indicator of what the problem is, the QNX overrides. They simply do not work.
Previously I saw a number of very strange results, eg. libraries not being found, although they were were they were supposed to be and being pointed to.

I do not have the knowledge to fix this, and I suspect I will have to throw out the baby with with the bath water.

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http://community.qnx.com/sf/go/post100546
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