Japan is difficult to get out of cheaply unfortunately, the market dynamics here are a bit messed up thanks to so many local consumers not being terribly price conscious.
Garuda is available via DL or another Skyteam carrier. You could transfer some points to DL for that, though if going the points route I'd certainly go Business and not Economy. Even expensive economy routes, I can't really justify the point cost.
For the short haul stuff, definitely LCC is more efficient than points in that region. Even for the long haul, you may strike a deal on Air Asia or Scoot out of Japan but they're harder to come by.