Hopefully they will eventually draft an agreement where each FFP's members can earn points and status irrespective of whoever markets the ticket.
That said, as alluded to by JohnK, the problems will be consistency of earn. For example, Class Bonus is currently at 50%/100% extra for J/F on QF (marketed) services only (not BA and AA); going on the same trend suggests that EK would also "miss" on this Class Bonus and use the more default 25%/50%. Status Bonus is currently only earned on QF, JQ, BA and AA services; once again, a guess may suggest that EK services would miss out on Status Bonus, unless they are "close" enough to QF in this agreement to be included in that subset of airlines.
As for Economy classes that will earn at the 1.00 rate, QF will more than likely maintain the current trend of all Economy classes earning 1.00. With EK marketed tickets it may be different. I'd like to see at least 0.50 for cheapest Economy (vs. 0.25 for BA Y), and all classes earning something (viz. would be sad if the cheapest Economy fares, e.g. sales, do not earn anything if marketed with EK). The dilemma would be not much different to QF codeshare vs. marketed on AA or BA Economy, where often the earn rate would be 0.25 - 0.50 rather than 1.00, which would only be earned on full Economy fares.
Status credit earn (except for the overarching issue of QFFers earning them on EK marketed tickets) will otherwise be consistent, though if there are ever double or bonus SC promos, these usually work on QF marketed tickets only, so naturally there is a "minor issue" there.