We have been using AlignRT with cones for over two years. Blockage of the ROI by the accelerator gantry can be a problem. Make sure your ROI includes the side of the face going back as far as possible to the hair line near the temples.
We do not use AlignRT gating of the accelerator but we closely observe the patient and the accelerator gantry position. We can predict at what gantry angles we will have a camera eclipsed by the gantry and for those angles we tolerate AlignRT being outside our tolerance of 1 mm. Usually this only lasts for 5 to 10 s. If the patient is out of tolerance when we know the gantry is not blocking a camera, then we will stop the accelerator by hand and go into the room to adjust the patient setup so that they are back within AlighRT tolerance. Treatment is then resumed.
I hope this helps.