Erik,
Using Adobe AIR really only allows me to directly connect to the built in SQLite database. I can’t connect to an other DB with the built in AIR apis. There are some open source projects in the works that may help solve this limitation but for right now the only option for integration with other databases is to have an app server in between that Klok talks to. Then the app running on the app server could connect to whatever DB you want. This is basically how the 3rd part integration is working right now (in my unreleased version 2). I think this is what you are suggesting with the PHP based integration. The real trick with the integration is when the system is offline (without any internet connection). In this situation, I need to a way to remember all the things that need to be synchronized and then when the connection is available sync it up.
The real delay in V2 is the complexity involved with handling changes made in Klok and changes that might have been made directly through a 3rd party system. If all you intend to manage the projects only through the online system and are only going to add, update and delete time entries with Klok, it would be fairly “simple” to make that work.
Perhaps if there is enough interest in that, I will get that released sooner than the full fledged integration.