I've never heard of this being an issue and have earned points/SC from bookings both with and without my middle name, on Qantas and on partners (my QFF profile does not include my middle name)
As far as I'm aware, the only exact match needed is QFF number and surname.
@puchu if you don't get a favourable response from your follow-up email I would definitely give them a call. Make the point that you have already received points/SC from the flight you were involuntarily moved to, and you're just requesting they credit the earnings per the itinerary you booked. The Manila QFF team does have an escalation matrix, and if you push hard enough it will get escalated to a case manager who generally understands the actual ins and outs of the program, but it can take them up to 48 hours to call you back.