If you have the option for an epub book, pick that over pdf. Epubs will convert much better than a pdf will.
Yes, a pdf with no DRM can display natively on the Kindle, but whether it will look good and be large enough to read without zooming will depend on the formatting. The same applies to whether it will convert well -- it's basically a crapshoot based on that particular file and its idiosyncrasies. It might look great -- or it might have funny line and paragraph breaks.
If you have the choice, pick epub. Conversion is much easier and more consistent.
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