I think one of the problems quite a few people have about this is that they assume that once a communication - and please note, RIPA talks about communications, not messages or copies of messages - has been delivered or read then it can no longer be in transmission.
Traditional physical letters and documents behave like the stuff we played with as a babies - for instance they can't be in two places at the same time, or both hidden and in view - but electronic communications do not behave like those things, they can be (and frequently are) in many places at the same time, and most importantly they can have been delivered and still be in transmission at the same time.
Subsection 2(7) of RIPA is entirely clear on that point, a communication can have been transmitted and still be in transmission:
" For the purposes of this section the times while a communication is being transmitted by means of a telecommunication system shall be taken to include any time when the system by means of which the communication is being, or has been, transmitted is used for storing it in a manner that enables the intended recipient to collect it or otherwise to have access to it. "
Once you get your head around the idea that a communication does not behave like a physical object, it's all quite simple - but some people do have extreme difficulty with it.
Was the QC simply one of those with this difficulty? I don't know, and the question is clouded by the other politico-legal issues - if read messages are not protected by RIPA then the Police can do things which they cannot legally do if read messages are so protected, and they have plenty of motivation to want to accept "legal advice" which says read messages aren't protected, even if it's clearly wrong.
Perhaps it's all in the choice of advisor. The police choose who advises them - wasn't there a recent case where they employed a very dodgy pathologist in a case where there was obvious public interest and accusations of Police misconduct, or even manslaughter, and the most competent and upright pathologist available should have been chosen?