At first, this whole "folder" issue is totally frustrating. Then, when one realizes the zillions of changes in CC software (and HTML5) since 1996, it becomes obvious that CC has tried to come up with a solution that allows developers that use quite different "file trees" and operating systems, not just Windows 10 Desktop, like me, to benefit from the same meme.
Coffeecup Software (CC) could help us a lot with better search algorithms and flyover hints. NOTHING in the software packages (that I see) explains that valuable but dangerous .rsd .zip examination trick.

Regarding tooltip etc. hints, it may be helpful to post in the Site Designer Suggestions section which items need more or different help.

In the latest versions of Site Designer there are probably few web-design tasks that cannot be done entirely within the confines of a project (.rsd) file, especially since the introduction of the Content Code switching facility. In addition, the facility for replacing items in Resources makes the effort to change images etc. almost negligible. The difficulties mentioned in the early posts of this thread do seem to have been addressed in the last eight years.

The practical benefit for users of the program in examining the contents of a (.rsd) project file is not clear to me, and the absence of mention of this in the User Guide etc. seems unsurprising. Evaluation of search algorithms used is perhaps outside the scope of these user forums.

Frank