The only thing "flawed" here is your assumptions.
Beg to differ…
No my assumptions are totally correct. The error in the software is in the design; which makes it restrictive and illogical. If you read forum posts there are endless complaints relating to the extreme difficulty in managing music.
This is done *very specifically* to prevent people from pirating music and picking up malware by copying music willy-nilly with every computer hither and yon.
No, the software was designed to prevent competition and to create the need to purchase from the Apple Store. Most of the world is completely honest and will respect publishing rights. Those that are dishonest will always find a way to beat the system. (It isn't really hard to do.)
Without this fundamental protection, not only would you likely have widespread iPhone malware (of which there isn't any now), but there would be no iTunes Store, since it operates under license from the record companies.
Wrong again. Fundamental protection from malware is built into OS X not into iTunes. As for the iTunes store, you are making an assumption without logic or factual proof.
What was done by Apple support is essentially the same thing we were advising; they likely had you make a backup of the data on the iPhone, then erase and reset the iPhone, and then transfer the backup back onto it, now under the ownership of your present machine. Possibly they had you put the phone in "manual mode," copy the songs from it (like a thumb drive) to iTunes, then erase and re-sync, essentially a slightly different route to the same procedure.
I told he Apple tech that all the information on the iPhone was expendable. Initially I was hoping to retain the data on the phone but after repeated failure at applying a ‘fix’ I was more than willing to wipe the phone clean to expedite the process. Truth be told, he was at a loss to explain the reason for the difficulty I was having.
Finally be aware that at one point I loaded a (legally purchased) cd to iTunes and was unable to move it to my iPhone; clearly having nothing to do with prevention of malware or pirating.