LANDESK does try to provide the bits for as many applications as possible. For a complete list, see (Article Replaced) LANDesk Security and Patch Manager - Product / Content List Report. However, as you've noticed, applications that are updated via the Mac App Store, LANDESK may only be able to supply the definition as opposed to both the definition and the file bits.
You can definitely setup an Apple update server in your environment. You are correct, by adding the server URL to the Apple update server in the Agent Configuration's "use alternate update server" the clients will attempt to pull of their bits from that server prior to going out to Apple. So if Apple happens to be providing the bits for the applications you're looking for via their update service, that would be a good way to go. Furthermore, it will save you on external bandwidth as your clients would look local prior to going external.
Thank you for the response, Northice. I am going to try using the alternate update server option and see how it works.
I just thought of one more question. Some of the patches (like with iPhoto for example) require that the patch be downloaded and zipped up with a specific zip file name. Are we going to have to do this on the Apple server in order for LANDesk to see the updates as being downloaded?