Ahhh, so we blame the travel agent do we? If the agent isn't savvy enough to pass the information on, you wouldn't book with them again would you? (Despite the fact that the operator is clearly marked on the itinerary, with or without a codeshare flight number)
As AN flyer says, the t&c are there to be read before the "i agree" button is pushed. That includes the fact that luggage has to be collected & rechecked - hence you cannot book a connection within 90 mins if you are transferring from QF to JQ or vice versa.
As for
VB, if you book 2 sectors in two different bookings, you are picking up your bags and rechecking, even though they promote through check. Often there is a marked price difference ($200+ vs $79 in my example) booking a through itin as opposed to booking sector by sector - the price you pay is having to collect the luggage and recheck. Not much different to JQ in reality.
Tigga pax will certainly be in for some costly suprises if they haven't read their t&c! But, who's fault will that be?
Cheers