With auto align, if I change out any of my optics before beginning my viewing session (focal reducers, barlow, video camera, etc), I can wait until the system is aligned and tracking before focusing the new setup. This is especially helpful when using an Alt-Az mount since it does not begin tracking until the mount is aligned.
I have added a JMI remote focus control to my C8, which when used with the SSA allows me to get everything in place both outside and inside before I turn anything on. I then power everything on at the telescope, start the auto align process, go inside and power on my laptop and start up my video monitoring and control software. When the auto align is complete, I slew to a bright star and check my focus and am ready to begin.