I don't think that these problems are unique to the BA/QF relationship or to oneworld. People complain about this sort of thing in every supposedly-seamless airline alliance.
I've occasionally had similar problems with BA/QF, but they have been very infrequent compared to the number of flights I've taken, and they are relatively small problems compared to the real benefits of the alliance. Chief amongst those for me are the flexibility of "Valid BA/QF" even on the cheapest fares, lounge access across both airlines' networks worldwide (through QF Club), earning QF status (and hence business class check in privileges - and eventually lounge access) on all BA flights, etc. etc.
You can minimise the risks of miscommunication by only booking the code of the operating airline. I know that now reduces your FF miles earn (no status bonus) if you book the BA code rather than the QF code on BA, but I regard that as a small price - and status earning is the same.
Also, BA stations that check in for QF (notably LHR T4) should have a crib card at the check in desks which sets out unequivocally and accurately what privileges the various QF tiers should have. In any event, my own experience of BA check in agents (business class desks) for excess baggage has been great. On one occasion, I turned up with about 55 kgs (20 kg allowance on ticket). The agent said she'd have to charge me. I said that I should have an extra baggage allowance. She tried to phone a supervisor but couldn't get through, so shrugged her shoulders and just checked all the bags. An extreme example of the typical BA attitude, which keeps my money flowing towards them and QF. (At SYD, the QF agents don't even seem to read the total weights but that's another story.)
For lounge access, BA lounges have a similar crib card at the desk, in case there is any doubt. It's worth asking to see it if you run into trouble.
It's also worth printing out and carrying the oneworld Ruby/QF Silver privileges pages off the websites - should be just a couple of pages.
bealine: Unfortunately, the alignment of Frequent Flyer membership into Ruby, Sapphire and Emeald tiers was designed to eliminate exactly such a difficulty as the one you describe. I can only assume that either Q.A.N.T.A.S has "gone it alone" by offering something the other partners don't (in which case it doesn't apply across One-World) or the information hasn't been cascaded to those who matter - those employees interfacing with the customer!
It's true that it actually sounds less like oneworld problems, and more like problems when being checked in by BA agents for a QF flight on a QF aircraft, or for a QF code on a BA aircraft. Classic handling/codesharing problems.
But there are some BA stations which can't get the oneworld stuff right, either. My biggest oneworld problem has been that many BA check in agents in the US just will not accept that oneworld Ruby has business class check in privileges. And of course if you start off your check in process with an argument about whether you should be at that desk or not, it rather queers the pitch for any other sort of discussion. (At least on the last occasion I ultimately had the last laugh, from the pleasure of demonstrating to the agent her own incompetence in failing to pull my flight coupon.)