I think Jamie and Charles first 'real' meeting must be in the chapters to come. Of course, Charles may have been the Icarian visitor to Croal or Jamie might have seen him, without being introduced, at one of the various functions he attended, I am sure anyone else there would have been more than eager to fill Jamie in on Charles' power and supposed evil, certainly Miro and the other Gahdar would know all about him. And you know what irrepressible gossips they are .
I don't think disunion inevitably leads to madness and death, that outcome is just very likely. I am sure that at one point Jamie asks Niklas to fight disunion should anything happen to Jamie and protect Charlie. Given a great enough responsibility or need I think it can be overcome.
The question of Jonathan is very difficult. Jonathan's condition is almost certainly not accidental or a by-product of a failed experiment. Like Jamie, Niklas and Charlie he must have been created outside of official empire view and like them was created for a specific purpose with specific attributes in line with Croal and Jonas' plans. Indeed it would be very Croal-like for Jonathan to be created as Charles' genetic brother in order to ensure he always had powerful protection, just as he did with Jamie (the shield) and Charlie (the weapon). The interesting question is where has Jonathan been.
I suppose he could have been a 'failed' experiment in that it is fairly obvious there were people in Gold Glass who actively assisted Croal and the resistance and his real 'adjustments' were done secretly with the failed experiment as cover. After that he would have been spirited away and hidden while officially terminated. Alternatively Charles may have been allowed to keep him if he was a true genetic brother, even if a failed experiment, but given the attitude of the empire I think that unlikely, certainly if that was part of a plan to keep Jonathan safe it would have been a very foolhardy one, not likely to succeed.
Also remember the empire's watchword when creating avionnes was perfection, imperfect production was terminated as happened to those unfortunate to be born blind in the vision experiments.
Let us hope there some answers in the not too distant future.