Hi,
You state that certain software conforms to one "convention", whilst other programs conform to "the other convention".
As far as I am aware, there is no such "convention" defined anywhare - plese, someone correct me if I'm wrong.
The manufacturers of imaging devices, at component level, have some notion of where the (0, 0) position is, and in which direction things 'count up' (i.e. rows before columns, or columns before rows, etc.). Then a camera manufacturer selects that particular imaging device and has the freedom to impose whatever convention they choose to use - they do not have to adhere to any conventions whatsoever.
Now you add an external software package to control the camera and to download the (un-)conventional images taken by the imager. Guess what? Yep, there is, again, no convention whatsoever that specifies how that image should be stored on disc - or, rather there are a host of conventions that could be used, none of which has any greater standing than any other.
Foryunately PixInsight knows this, and gives the user the flexibility to apply an over-ride to the stored data such that the user is then given the power to impose their own 'convention' to the data typically acquired from their imager.
Of course PI provides the ability for the data to be 'mirrored' - in fact it even allows for 'both' types of miroring - in either the horizontal or vertical direction (these two actions are known as Flipping and Flopping - although I can never remember which does what !!!)
So, unless I have missed some crucial point in your brief reply, I hope that this has been of some help.
As to release of a manual, is this really necessary given the wealth of information already released and published about PI. If one were to be released, just exactly how many people would read it? And how many people would refer to it more than once? It would ultimately just be as useful as the manual for your PC, your Operating System, your Toaster, your TV and even your Car.