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If your source formats give equally good results then I wouldn't have thought it matters which one you select.
However, I am interested in why you have selected PDF and plain text for archival purposes. These would be some of the last formats that I would choose for an archive: PDF because of the lack of reflow; plain-text because of the lack of formatting.
ePub would give you reflow and also supports a lot of formatting. Maybe you have other requirements that require PDF and plain text?
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