The problem you are experiencing with the vertical disparity at the point of the instrument transition is caused by a problem where a vertical staff spacing adjustment is somehow being applied to one instrument and not the other. In Engrave mode, enable the staff spacing tool, then select the handle corresponding to that staff and hit Delete.
Regarding condensing for players holding multiple instruments, at the moment only the first instrument held by a player can participate in condensing. There’s nothing you can do about this at present.