My thinking is that the actual issuing of tickets will remain unchanged (i.e. the coupon tickets we've had for decades) and that the online system will simply generate a pick list of what the customer wants, to be processed by the booking clerk in the usual way.
There is no reason why Stena Line and Irish Rail shouldn't be able to do likewise. The system required would essentially be the same leading to the possibility of a centralised SailRail booking facility (just my point-and not based on any knowledge/assumption that this will ultimately happen).
My only concern is that the online system wouldn't become the exclusive means of booking SailRail. Hopefully the online system will attract a strong level of bookings but the facility for booking in person at both the ports and certain provincial railway stations needs to remain (internet great but does not suit all people at all times in all places). Too often these days the assumption is made that everyone can do everything online.