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Boycotting Amazon as part of a wider movement to convince them to be more open -- or at least to not actively support their closed spec which necessitates reverse-engineering by people who could spend their time doing more important things -- is certainly an option.
And I am not going to say you shouldn't do that.
But it didn't answer the question of "how to future-proof".
Storing your files in EPUB makes no sense though, I am afraid. calibre is open-source and already supports both AZW3 and EPUB, so there is no "most likely".
Store your books in the original format, whether that is EPUB or something else makes no difference.
Conversions are inherently lossy, so always save the original copies and work from there. Same reason why you save music as FLAC, and images as RAW.
You could, however, argue that you should purchase in EPUB.
But converting from AZW3 to EPUB in the name of storage/backup and future-proofing is simply silly.
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