We can look at suggestion 2.
As far as suggestion 1 there is nothing I could do about that. That is merely how the download works. When you open the zip you see there is no directory so the proper action would be to place the unzipped files in there own directory this is what I have always done since I first because a customer 9 years ago.
The way the members download script works is I upload a source file which has a directory say called pp-classifieds52 in there with everything. There is a script on our site which goes through and encodes your license number through all the files and it is that script which compiles the final download and that always processes the code into what you see.
I will pass along your comment though on the download. If we did not have to worry about encoding license numbers into the files I would easily do something like that.