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There are several spec's defining the creation of digital content. They apply to e-books. To meet these spec's requires the creation of several files (opf, toc, ncx, content,etc) which control the building of the e-book. Any application that purports to produce an e-book in a specific format (kindle, epub, etc) which does not use these files, is only meant to produce a document which can be displayed on a Reader device for the owner's personal use.
Applications such as Kindlegen accept an OPF file as input and build a document following the instructions in the OPF file, whereas applications such as Mobi Creator do not, although Mobi Creator can produce a PRC file which a Kindle Reader will display.
Other formats, such as EPUB, also use opf, toc, ncx, content files, etc to create e-books and if the application, or method of packaging the e-book meets the digital spec's, the same construction file can be used with only slight modification to accommodate different Reader devices.
In brief, if you want to construct an e-book that meets digital spec's, and can be used to build versions that will run on more than one Reader device, the construction files need to be hand coded. If a translation application is used, the output can be read on a users Reader, but is unlikely to meet spec's, and probably can't be used on another type of Reader
Tony
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