One of the things I've wondered about is, when did Jamie and Charles meet exactly. To my knowledge, they haven't met yet in the story and can only assume they will be meeting soon. We do know that Charles has known about Jamie for a very long time, but didn't know about Charlie.
We do know Charles had a mate at one point, but I think the big questions is, were they a mating pair? If they weren't, that could explain why he doesn't appear to suffer disunion. The rose bush in his garden was set up as memorial to his partner. What makes me think of this comes from one of the chapters after Christophe's death where Jamie finds out from one of the Trio that he loved Christophe and he refused to mate due to being in the chair.
Jonathan could be Charles brother biologically, or in an adopted from. Jonathan could also be from the experimentation that was done on vision which failed, but had an unusual side effect in which he was still able to see, just differently from everyone else. We've seen this demonstrated in Book 1 during Nic's birthday celebration.
Perhaps Gold Glass was trying to enhance the Red and Blacks and Jonathan was the end result.