A versions are made using finer process, so take less silicon. Non-A versions are likely to be old stock, so they are probably were purchased by Mouser at a higher price, and they want to make their money back.
There should be no functional differences as long as your device is within specified ratings. I've seen boards where A version would fail if installed instead of non-A version, but in all of those cases absolute maximum ratings were exceeded (hi to all the people, who think that it is OK to overclock the micro).