I was just about to come back here and mention that. The article and comments that @stevekemp linked to provided a lot of insight, but as you mentioned, there are ways to prevent exploits of that nature, which the comments in the article point to also. Something still seems to be missing from my understanding of what Skype is doing...
The cynic in me thinks this is already known and is in use by a "strategic partner" as a vector. The next version will only make it harder to find and exploit.
I doubt this was intentional at first, but the fact that they don't want to fix it is very fishy.
That is a very different issue, as there the concept is that the original file in the original location is being replaced. As is stated in that post, at that point the person could just as easily replace the program itself with a modified version of the entire program. That is not a security issue in the software.