Noone is suggesting suppressing material facts.
That is the road to a world of pain.
The point is you appear to have acquired PR by say 2009 or 2010 so what you did later is immaterial - as long as legal ofcourse (and leaving morals safely to one side).
So the fact you had no CSI at a later date is immaterial.
So no harm in declaring your period as a student.
You can add a cogent cover letter if you wish, to really spell it all out and spoonfeed the caseworker.
However, don't focus on what you didn't do - simply focus on pointing out your qualifying 5-year period.
Suggest start here, by taking a look at this example PR form a member has compiled by mashing a previous/simpler PR form with up-to-date HO contact and other details:
https://dl.dropboxusercontent.com/u/128 ... ple_v2.pdf
Suggest printing a few copies and trying a few dry runs with your information (& all supporting evidence) - see how it all shapes up.
Note: it may help your nerves and sleep pattern if you steer clear of the HO helpline; however well-meaning, the advice can often be misleading and contradictory (as you appear to have discovered);
furthermore, the advisors are not held accountable for it.
As to the privilege of citizenship, you can monitor the forum but I'm not aware of anyone being refused on 'moral grounds' for not having CSI after acquiring PR.
Applicants can and do ofcourse fail to acquire PR/fail in naturalisation applications by
not having CSI when relying on a period of study to exercise treaty rights.
That is a different scenario from yours so what I've just said is to
reassure you (!).
Worst case, now that a 'confirmation of PR' card is mandatory for naturalisation, you are risking less than £100 to discover any issues.
And as you have worked continuously for at least 5 years since 2004 you shouldn't have any issues in that area.
Good luck.