The changes don't have a great deal of practical impact, mostly being a tightening up of the spec words. Joe has a colourful diff of the protocol changes, the format changes correspond to closed issues on the AtomPubIssuesList.
W3C response to proposed Atom Publishing Format and Protocol (atompub) working groupEric Miller :
The W3C agrees that Atom is an important developing application. We feel that its specific relevance to the Web, however, indicates that it may find more success in a standards setting organization with work in similar areas. Due to its close relationship to the range of Web-based technologies, we suggest that the Atom community propose to do this work in the W3C.
The issue of bad-feed handling came up again on the mailing list, and this time had a positive result: PaceServiceError is a proposal from Robert Sayre, which "specifies a new AtomAPI endpoint by which Atom clients may report invalid Atom documents to a server. "
In other words, if a client spots an error (e.g. ill-formed XML) in an Atom feed, there's a now place it can go to report it.