I think we might be confusing the issues here. If something happens to your computer and your hard drive goes kerplunk, when you re-download iTunes and attempt to transfer your apps back to your computer from your device, it no longer works. Your only option is to re-download every single app, song, video and ringtone to your computer. Even if you have your entire iTunes library stored on your iPhone, it does you no good - you have to re-download everything.
Same thing happens in the other direction: if you buy a NEW iPhone and you have everything you want on your library in iTunes, the apps will not transfer over. The backup will map out what apps should be on your new iPhone and where they should be (ie - what folder they should be in) - but iTunes will not actually put the app on your phone. You have to re-download it to your phone.
I was on vacation when I purchased the new iPhone 6s. I had my work laptop with me. I made a backup of my iPhone 5s to my work laptop and none of the apps, music, videos or ringtones transferred over to the PC (which was an authorized PC). When I hooked up the iPhone 6s, it received information on which apps it should have and where to place them, but then began downloading them, one-by-one, OTA. The music and ringtones were also not transferred.
I had a huge playlist of songs that I had made for that vacation that I could not put on my new iPhone without re-downloading every single song to either my work laptop or the iPhone - even though I had an iPhone 5s sitting right there with everything I wanted on it.
I gotta say - this time around, things most certaintly did not "just work".
I came home from vacation having to download the rest of my apps, music, videos and ringtones on my WiFi network before I had a "complete" iPhone again. And don't get me started on the data overages on my mobile bill...
EDIT - Correction, the music, videos and ringtones that reside on your hard drive DO transfer from the PC. The apps do not. I didn't have to re-download every song, video or ringtone, but I did have to re-download every single app.