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I'd do it exactly the same: buy a book where it's cheapest, or in case of free public domain classics, where the layout is best.
Because most, if not all tools are geared towards creating and editing EPUBs, I immediately convert each book into that format, and clean it up/edit it with calibre and its editor. Yes... even if I buy a book at Amazon, for reading on a Kindle, I STILL make an EPUB out of it, clean/edit it where necessary, and then convert it back into AZW3 for use on the Kindle.
My library contains books that originally were LIT (from the old BAEN free CD's), MOBI (some of my very first purchases at Amazon, some from the BAEN CD's IIRC), AZW3 (later purchases at Amazon), and EPUB (mostly Kobo, but also other stores that are gone now).
All of them are freed from DRM where necessary, converted to EPUB, cleaned, edited, tagged with metadata, and shelved in the calibre library.
I therefore don't care what native format an e-reader uses, as long as calibre can convert to it... if not, I don't buy the reader. For a pure EPUB reader I'd obviously not convert. For my Kindle, I convert to AZW3, for the Kobo I convert to KEPUB because I like it better than the EPUB handling.
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