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It gets a little more complicated because not all mobis are equal. My understanding is that there are two different book formats that can be in a mobi. One is the "old" inferior format that is commonly thought of as a mobi file. The other is the "new" format that is either similar to or the same as what you will find in an azw3 file. You can also have a "dual" mobi that contains both formats. Either a "new" or "dual" mobi will behave like an azw file on a device that can handle the AZW3 format. One advantage of a "new" or "dual" mobi is that you can use them with Send to Kindle.
As far as a difference between different AZW3 files, different conversion programs will give slight differences, but should overall be pretty much the same. So, technically, yes, there will be a difference between a legit retail version and a converted version of a legit file that was converted. Most of the time, I don't think it should be too significant of a difference, but I'm not anywhere near expert enough to tell you what those might be.
If it is a "new" or "dual" format mobi, I would recommend leaving it as it is, unless you want to use the hyphenate this plugin to put in soft hyphens to improve hyphenation. If you have a recent firmware version on a Kindle device, you can tell if it is a "new" or "dual" format by loading it on and see if the boldness options are available.
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