Well If that is the case it needs to be made clear to passengers by the wording on the ticket which it is not....
I would have thought that such a distinction would be made at the time of purchase, but then if you asked specifically for a ticket to a Metrolink destination, why would they think to tell you it's not valid on that part of the railway (especially given the rail only fare is generally cheaper).
....I used to regularly use a Hazel Grove to Metrolink Zone F ticket via Navigation Rd, and had no problems doing so either from Northern guards or Metrolink ticket inspectors....
I'm not sure a Metrolink ticket inspector would care what route you take, my personal impression of them is that they only care if you don't have an in date ticket, although I am happy to be corrected on that.
A Northern guard might not care, notice or know the distinction, they may consider the ticket to be off route rather than deviation to a new destination or over-distance. Off route would certainly be less work even if not strictly correct.
....but I have been unable to find it written in any publication to say you must interchange at Manchester stations, nor can I find anything in the NFM. So I would argue it would be allowed, even if it is not the intended interchange....
In the PTE section of 'The Manual', it states that they are add-on tickets for the Manchester Stns fare. It is also known that from Altrincham there is a rail ticket to Manchester and a Metrolink ticket (both available from any National Rail ticket office) but the Metrolink one is not valid on the railway between Navigation road and Manchester and the railway one is not valid on the Metrolink (from/to Altrincham), the same applies to Plumley, Knutsford, Ashley and Hale.