There’s really no point in transferring the file: it is not ‘source of truth’ for what the highlights and notes are. For example if you switch to a different device and make notes there, the log file won’t have these. And if you delete highlights or notes, the log file does not reflect that. The source of truth is in the cloud, better to trust that.
Using clippings file as source for import after conversion is not at all ideal. Kindle can export them on demand as an email attachment in a more structured form (.csv plus .pdf) that is more amenable to whatever tools you have to convert and migrate things. That said, I don’t know what is possible in terms of importing notes should you choose a different reading platform. Kindle platform doesn’t have a way of doing it, for example. There is a draft specification for ‘Open Annotation’ in ePub for example but I don’t think it has any implementations:
http://www.idpf.org/epub/oa/
I think the use case for exporting notes is to make them more readily accessible for using them in whatever writing you might be doing (reviews, academic work etc), or just so you can compile them somewhere and review them more easily.
Of course, having a document with the highlights and notes would make it easier to re-create them on a new platform, but I would not expect it to be effortless.