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Sorry, but I have to disagree with you about this.
First, such a log file would not be of much use, if any. If you are not sure that an automatically generated MOBI file is OK, it is preferable to test it with Kindle Previewer. There is a problem with consistency and common sense. By converting an EPUB file to MOBI, Atlantis saves a user a couple of mouse clicks or key presses. Those who have difficulties with running a command-line utility, might find this automatic conversion useful. But they would never need to play with a cryptic log file.
Second, as far as I know, kindlegen.exe does not create log files. It does display various warnings in its console window. Capturing text from a console window which normally displays for a second or less, is possible, but it is not a trivial task. Sorry, but I think that it would be an absolute overkill. Especially when there are simple workarounds.
By the way, Atlantis does its best to generate Kindle-friendly EPUBs. If your EPUB displays correctly in eReaders, there are good chances that a corresponding Kindle file would also be OK.
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