Charles and Thomas go on lackey missions together for the senior templars, so they do spend time together travelling. They have sex, but it means nothing, aside from keeping them from getting at each other's throat in more violent ways. Charles keeps Thomas in line and Thomas lightens Charles' mood. When one is in trouble, the other makes sure to quickly put an end to it - for reasons of the brotherhood only, of course. And Thomas might actually have petted Charles Lee's pomeranians a few times.

Someone points out they are dangerously close to approximating a relationship. Charles and Thomas are (even) more surprised and annoyed than everyone else because they realise its kind of true.