All versions of PD "hard code" the file address within the .pds file. Actually, but sometimes not practically, the .pds file can be edited in a plain text editor to substitute the initial addresses with any "new" addresses. As far as I am aware (but I stand to be corrected) when a media file is "active" in PD it is "locked" (my word) so it cannot be moved or renamed but it can be copied.
Whilst I take your point on your preferred organisation system, the cost of storage is so cheap that there is merit in examining alternative "project based" organisation systems to minimise the issues you have identified particularly over a couple of years, as I (and probably many others) have certainly lost track of asset locations for long past projects.
The export>pack procedure is a good discipline to implement whenever possible.
Cheers
Adrian
Life is really simple, but we insist on making it complicated. (see below)
Confucius
AMD Phenom IIX6 1055T, win10, 5 internal drives, 7 usb drives, struggling power supply.