The JAA situation goes back to when Japan began recognising PRC
as China, in place of Taiwan. The problem was that although air travel between Japan and Taiwan was (and is still, very) lucrative, you have to recognise the country with which you're operating a bilateral agreement. So, the compromise was an offshoot which didn't have the Japanese flag on the tail; it was a convenience carrier, purely for the purposes of operating the route.
Many other carriers had the same situation; Australia/Swissair/British Asia all were subsidiaries of the main carrier - QF
/SR/BA, but they didn't have flags on their livery and in the case of BA
, where the flag was part of the tail design, it had to be changed. (Interestingly, SR
's cross caused it some problems in flying to Saudi, as they get upset at anyone else's "religious" symbols).
As for QR
, both have started services to Shanghai, so that might be part of the reason, but another reason might be that BR
operate to DXB
already and there may simply not be the market for EK
; can't believe the market from DOH to TPE
is not great.