Thanks for the replies, and especially to Francis for clearly differentiating the aspects and responsibilities of the NGiͶX "flow", if I can call it that.
The only remaining confusion comes with the provided nginx config files which appear to contradict best practice (as well as setting up parameters which don't even exist!) , but I now realise and acknowledge that this will be an issue for the Ubuntu NGiͶX package maintainer, not NGiͶX.
I think what I might do is to do another complete brand new install of NGiͶX and PyroCMS, see what the most minimal config changes I can make from the default are for my application, test the hell out of it, and tentatively make changes to the Wiki page for the Pyrocms config.
Thanks again. PS - as I post this, I see below that today has set a new record for numbers of users and guests on the forum. Excellent!