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OK, clearly mobiperl isn't going to do what you want. And you won't spot differences in the HTML as that's not really the important bit. If you use MobiUnpack with the appropriate flags to dump everything, you'll see that in your example from mobiperl you just have the Mobipocket header, html, ncx and opf sections in your generated file.
In the one from Kindlegen you also four INDX sections, a FCIS section, a FLIS section, and three tiny unknown sections.
If you want to build a Kindle dictionary without Kindlegen, you're going to need to reverse engineer the compiled dictionary format, and then create something that can build it. No easy task!
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