I naiv assumed is that one of the reasons for the slowness of the 3640 might have just been "time-to-market".
E.g as soon as it worked it was sold - without giving the developers time for tuning.
As it's commodore, you can assume they sold it before it worked. An insight into what was going on at commodore at the time
http://www.wonkity.com/~wblock/a4000hard/defibust.htmlWhether those wait states are ever required is something that anyone doing this upgrade will have to consider, with the hack it might only work in a limited combination of a3640/buster/motherboard/phase of moon etc. If it works for you and you don't have an issue modifying classic hardware then I don't see the problem. If you have problems in the future then it will always be the first thing that you will doubt.
Dave was human, he made mistakes. They might have been added under an assumption they were required, or they might not even have been intended. You could ask him, he might remember.