Running from SVN (or another source control server) makes sense if you are using released branches. It makes sure that critical security updates, which happen to scripted web applications far more often than binary applications, are applied frequently. Since most customers use SVN to pull down updates to web apps, you will often find that the apt-get repositories (or other distribution repositories) update less frequently and you will miss out on new features and security patches. Additionally, as web applications tend to 'mutate' rapidly and introduce backwards-compatibility breaking updates frequently, when the package does finally update you'll have a greater chance of having your specific app break.
As an example, Apache 2.2.11 is the current version, released last December. IIRC, my only Ubuntu server, which is hosting one specific application, is running 2.2.8. I can't seem to find a handy table for release dates in the httpd-2.2 branch, but the archive site says that changes-2.2.8 was published in early 2008. In that same period, the Zend Framework trunk grew from 50k lines of code past 20M lines of code.
If I were you, I would use svn:externals with the base package, and then add your own modifications to the subversion repository and stay up to date on security warnings that deal with whatever your web app's dependencies are. If you're into continuous integration, you can run the test suites in your environment and with your modifications so that you're aware when various trunks and branches are stable against your specific uses, and can update at will when security vulnerabilities are found.