It's difficult for us to improve upon our support for users on shared hosts, because there is no standard method of access; some provide SSH, some provide FTP, some only provide web-based administration tools. Unless SSH is available, modifications will be a headache. We try to address this by 1) testing on a variety of platforms, so that maintenance issues, e.g. the need to apply a patch, are as uncommon as we can make them; and 2) helping people make the changes manually when needs be.
Shared hosts have unfortunately been slow to adopt the newer, fixed releases of Zend Optimizer, so in the meantime work-arounds are still sometimes necessary for that issue. A patch file is the best and most widely accepted way of distributing a code change, but unfortunately it may not be easy to apply it on a shared host. This is true for any web app on a shared host, e.g. Drupal, MediaWiki, etc., and reflects more on the limitations of a shared host than on any support limitations.
If you're on a host that only allows FTP, the best way to patch an installation is 1) to download the affected files to your local machine, 2) apply the patch there, and then 3) replace the files on the server with your patched versions. Unfortunately, there simply isn't an alternative, but I can help walk you through the process.
Public Knowledge Project Team