Re-visiting Miyoka Harbor, I've done an experiment with eliminating the Jap_HarborTraffic.mis from the game by renaming it with a DOT BAK appended to the name, and ran a newly created mission with a Tambor boat sitting just outside the bay's mouth, and got this:
Go figure. Armageddon has been termporarily avoided... the file is commented out in the Campaign.cfg, but it loads somehow. Further experimenting is called for, and we'll eliminate the beast one way or the other...
Edit: Fix finalized and will be submitted for next round of updates... the original segment in Campaign.cfg has been deleted, instead of just being commented-out...