It'd be most accurate to say you rigorously described a kind of mining-cartel attack that had been discussed years earlier, but I know I won't convince you of that, because you only count published academic papers, and the earlier discussions of the same attack all happened in less-formal bitcoin forums.
Regarding MtGox scenarios:
Reliable evidence on what MtGox truly did is scarce, but people have widely speculated that at times they auto-reissued payouts, and without the protective measure of reusing the same inputs. It would be in character – see other examples of their recklessness below.
So while I share your doubt that malleability could have resulted in significant losses, there is a theory for that, which doesn't require extensive social engineering/human-in-the-loop processes. And, if it had been happening for years, only outsiders with a giant archive of long-ago race-losing transactions (that never reached blocks) would be able to estimate the magnitude of the losses. (I don't know any public source for such an archive.)
Similarly, at times Karpeles mentioned that the cold storage was a "paper-based RAID" in 3 parts, or some other scheme in 6 places. As the 'key man' in an enterprise that suddenly found itself atop $100MM+ in easily-transferable assets, his feared threats may have included kidnapping/extortion to force disclosure of the keys. Thus his cold storage scheme may have involved putting necessary key-shares totally outside his easy control, even via people and safety-deposit boxes in other countries. Any "key-loss" scenario should consider the chance law-enforcement-actions or other calamities, far from the MtGox offices or Japanese accounts, have made essential parts of the cold-storage keys unrecoverable, for now and perhaps permanently.
There's a forum thread from years ago where people mention 2600+ bitcoins MtGox lost from their own bad-transaction-issuing code (https://bitcointalk.org/index.php?topic=50206.0;all). Karpeles wrote his own SSH server in PHP. Over the years MtGox suffered SQL injection & cross-site scripting attacks. In the June 2011 'flash crash', the entire user database with weakly-hashed passwords was lost (supposedly via an auditor compromise), allowing outsiders to carry off some unknown number of artificially-cheap bitcoin – but MtGox made customers 'whole' via a database rollback. MtGox later that year made the customers of competing exchange Bitomat whole, at a cost of 17,000 BTC or more, after that exchange lost its keys.
So when speaking of MtGox, we're already in Alice-in-Wonderland territory, with both custom (and often unwisely eccentric) implementation choices, and overconfident grand gestures. It's hard to rule anything out, based on ideas from elsewhere about plausible engineering or business practices.