Well, at least the reason why legacy packages fail to show up on FW 3.4.1 isn't mystical anymore:
The legacy Python packager used the max value of a *signed* 32bit integer, instead of the *unsigned* value of such an integer (i.e., 2147483647 vs 4294967295) as the target OTA version, and since the OTA version of FW 3.4.1 (2540470001) passed that halfway mark, anything packaged with the legacy packager fails the version check.
(KindleTool does things right, FWIW, which is why I linked to the repacking post
).
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Spending so much time staring at the data types used in OTA headers paid off once again ;p.