If it is only the SysEx header that differs, use StreamByter inbound and outbound rules to modify the header as needed. I have done this in one Roland layout. Same length header is trivial. However, the Juno X and RD-88 have an additional byte in the header (Roland five bytes), so it is a little more complicated, since you have to move everything following the header one byte forward or backward. I will add posting the flexible version of SysEx header substitution to my backlog.
For big layouts, a SysEx search and replace function could be useful, for exactly this reason. May add to the list of user requests, but I would not hold my breath, since there is a lot in queue, and since there is a functioning workaround, isn't a critical upgrade.