Natstrack, I agree wholeheartedly with most of your post, except that point of manual flying in the initial phase of the A320 TR has it's greatest benefit (I feel) in introducing students to the slightly different handling characteristics of a FBW aircraft, as well as letting them get used to the EFIS and SOPs by flying using familiar principles.
Students on a TR can be new to jet engines, new to EFIS, new to heavy(ish) aircraft and new to FBW - often simultaneously! These are all concepts which can be eased into at first by building upon the 'basics' without initial use of the APFDS.