I seem to remember reading a post from a while back where someone else was also requesting a separate hidden folder for manifest files (possibly on the irex forum) and the responses where clear that the format was not going to change. I think there would probably be a greater risk of the additional info being disassociated from the PDF files and things could get very messy for some users, so I think the current approach is probably safer.
For me creating the container folder and manifest file is not hard work or time-consuming. I have a script that does it all for me that is integrated into my file manager so it takes barely a second to do it, certainly less time than it takes me to actually save the PDF in the first place. I believe that windows is more limited when it comes to scripting, but my script is pretty simple and it should be possible to reproduce it as a batch file or if not there is a version of bash.exe that runs on windows that could do it. I have no idea if it is possible to add a script/batch file as a right-click option in explorer to make it easy for regular use.
As for searching and reading: do you use a bibliography manager? Many now have a field for a link to a PDF copy of an article. You could have that link pointing to the PDF in the container folder and use your biblio software for searching and opening PDF files. (And what are doing reading PDFs on your PC now that you have an iliad!!!
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