Both of those side effects are most likely from the Chemo and not the Proton Therapy.
The Proton beam should be very narrow and have mostly localized effects.
Does the picture at the article show the type of machine that they used?
At LLMC he machines were referred to as Gantrys.
All of my treatments were carried out in Gantry 1.
The machine I was treated in looked somewhat similar to the one in the picture.