Is it possible to recall factory presets with System 6000 Integrator?
No, it is not possible to recall factory presets. You will need to copy the ones you want to use into the user bank. The user bank with Scene/Routing/engines can be saved into your DAW, so you can have a new user bank with each project.
A work around to using System 6000 integrator is to directly dump via MIDI the scenes on a MIDI track in the project. In this case you can use factory and user presets in the scene.