In addition to hat Tony said, keep in mind that using channel conversion means you cannot use MQAMS or any other encryption, cannot send binary-encoded messages, etc.
It's possible to write exits to handle any message types not converted in the channel but as Tony noted the app getting the message might not be the same CCSID as the destination QMgr. That requires the exit to work first in the channel and then again during the application GET.
Channel conversion is best used in the case of a point-to-point channel with limited, well-known types of messages. It's a narrow solution to a narrow problem. To enable it on a cluster is about the polar opposite of its intended use. Not that it's impossible, just rarely done and requires significant discipline to vet any and all applications to ensure they will not send unconvertible messages and bring entire nodes to a halt, or worse (if the repositories are not on dedicated QMgrs) the whole cluster. You did put your repositories on dedicated QMgrs, yes?