So, looking to get some clarification.

I see many MR to CGK at very good prices. My question is do you still earn the miles on the flight that is being operated by Japan Airlines. (or other code shares)

Tried doing research on AA.com and it seems that code share airlines allow you to qualify for miles at XX% of what is actually flown.
For example Japan Airlines:
Y, B =100%
H,K,m = 70%
L,V,S,G,O,R = 50%
N, Q = 30%

So, basically if you are flying on AA metal (coach). You are not getting 100% of the miles flown? This obviously really limits the value in doing a MR on JAL or even BA.

Or is this only for earning reward miles and not for Elite Qualifying miles?

Current Plat looking to make the run towards EXP, but don't want to do a MR and end up only getting 30% on a 2000K mile leg.

Thanks