While aiming for the 10mil rupy trophy, I've been using Karteira on my front lines to leech some extra rupies off slimes. After double-checking Gamewith, I can confirm that the rupies gained through Two Birds, One Punch can be affected by rupie journey drops.
My highest yield so far has been 46,135, which is far higher than the 13,500 previously listed on the wiki. Before that, I also got 15,000 rupies twice, but didn't manage to screencap those.
Edit: Further testing also showed that rupies gained by this skill are counted as rupies gained in battle (thus boosted by Karteira's EMP passive), rather than being counted as a "flat" rupie gain that is immediately added to your inventory. Killing a small goldslime net me 2888 rupies; using Two Birds, One Punch yielded 15,540 rupies for a total of 18,428 under the Loot Collected section of the battle menu.
