I guess Floortje described the setup process in perfect way and also addressed some of the technical pitfalls like shadowing effects.
Concerning your problem with MAG tolerance. It also might depend on teh software version you are currently using. In version 1748 you have for vrt, lng, lat and MAG only one comon tolerance which is somewhat unfortunate. If vrt, lng, lat happen to be all close to the tolerance, e.g. 3mm, then MAG will be out of the 3mm tolereance. Because of this shortcoming, we do not use automatic beam gating. However, with version 1749 you can choose individual tolerance levels for all coordinates, as well as for MAG. So in this situation you can choose a larger tolerance for MAG which might solve your “maged” out problem.
Other than that, you will probably always be confronted with “difficult” patients which cannot keep their breath level despite good coaching. That’s reality in clinics! I think it is important that you check your (BH-)setup with imaging and make sure that the thoracic wall is lined up well with your reference DRR. The goal is for sure to reach the correct vrt level (via correct amout of air intake) without adjusting the couch vrt after setup in FB, but in case the patient does not manage to reach the correct level it might be apropriate to rise the couch a bit such that the thoracic wall is lined up again with your reference DRR. Like this you make your that the ptv is within your treatment field. The drawback might be a bit more dose to the heart but it will still be better than treating in FB.
Maybe this helps a bit, Daniel