However you download from Amazon, it is the same book, same version.
(Recent ereader firmwares are beginning to download versions optimized e.g. for image resolution/size, but the principle is the same.)
As long as the book has not been further converted, it will have the same ASIN, so the device will see it as the pourchased copy, and sync the annotations etc.
Updated versions need to be updated manually on
http://amzn.com/manageyourkindle (you can also set this to automatic) but will then message your Kindle to delete the current copy and download the new one. This too is handled via the embedded ASIN.
...
Why do you get a different copy when downloading via Kindle for PC?
Well, you apparently downloaded a MOBI instead of an AZW3. Not sure why, I thought Kindle for PC supported AZW3...
Or maybe it is a dual-MOBI (has both AZW3 and MOBI inside).
Due to having several generations of format, and needing to maintain support for various past and present device models, the specific format you have can get a bit confusing.