My experience is that when I've travelled with a friend on a completely different ticket I simply need to call the plat line and tell them we are travelling together and the bookings are linked. When my father called (same surname, QPS) to link his booking to mine he was told that we should do that at checkin time. Given the disparity in our relative status and the fact I was in the lounge when he called to tell me I walked up to the service desk and they were linked in 15 seconds. At checkin time in both cases we have been seated together and have been allocated seats based on my qantas status (worthiness to QF, random number generator etc)

I think the issue isn't with the booking system, it's with some of the staff