I went to a meeting with Andy Hayman of the Met last week. I have also discussed matters with a number of other people involved in the Criminal Justice system.
It does appear that the key issue that drove the claim that 90 days detention without charge is needed is the idea of preventing an ambush defence where suspects don't comment at all during the pre-trial period and then generate a defence at the trial.
The difference in the cautions used pre (and at) charge and post-charge arises mainly from Section 34 b) of the 1994 Criminal Justice and Public Order Act. It is not an entirely full reading of the act and it may not be the case that primary legislation needs to change to handle this, but probably such a change would be useful.
I am still awaiting responses on this from a number of groups of people, but I think this could be a route to avoid detaining people without charge for even 28 days.