Can I reasonably ask that HMRC clarify exactly what their position is.
That would be eminently sensible. You can't really ask for help without knowing what the problem actually is.
The Officer will be following this guidance:
https://www.gov.uk/hmrc-internal-manuals/capital-gains-manual/cg64420p
I would say that the HMRC investigating officer has informed me that they would advise their management that they would not be looking for penalties which I take as acceptance that we are not hiding anything but only trying to minimise our CGT exposure under HMRC current rules.
That's quite generous of him/her. He/She might find that their manager disagrees, so he/she ought not to have said anything without authority. Clearly you haven't taken proper advice prior to the event and have not declared a gain that may be taxable. That could quite easily be construed as careless.