apt can't upgrade what it didn't install. You would run into the same problem if you downloaded PHP directly from php.net and compiled it yourself...
apt still wouldn't upgrade it for you.
You can either use the upgrade path that Linode StackScripts provide. (I wasn't able to find one by browsing their website.) or you can uninstall the StackScripts version of PHP and use
apt to install the one you want.
I have no idea how StackScripts will handle not being in control of PHP. You may want to uninstall StackScripts entirely and install Apache, MySQL and PHP through
If you have more Linode-specific questions, you may find more expertise over in their forums or IRC channel.