for example the different nature of the AP disconnect aural warning when anything other than the AP disconnect button is used
The only difference is that when using the takeover button the 'cavalry charge' only lasts for1.5 secs, when there is a FAILURE the cavalry charge is permanent. I have only ever had the AP on the A330 disconnect once when I didn't press the takeover button, it was due to turbulence, the cavalry charge did not sound permanently. Such disconnections are not uncommon on the A320 family.
I would hope that the SI would look carefully at the whole training package. If your reporting from your contacts in the unit is correct then there seems to be an unsubstantiated underlying lack of confidence in the aircraft and it's technologies. Training is but one method of establishing that confidence.
BEagle I admire your loyalty to your friend and that you have no doubts about him. I have never met him. Your reporting of events seem to have left some gaps in the narrative that were filled in by the interim report. I take it those gaps didn't come from him.