Sorry for the lack of update, my phone's battery died!
I'd actually got from Dundee to Manchester when I posted.
When I realised the machine wasn't doing ToD I went to the ticket office who told me I could travel using the booking reference. I then spoke to the guard when he came round, who was aware of the problem and said that was fine. I asked the guard about what to do for the second leg (Haymarket - Manchester), and he reckoned the connection would be too tight, so I should again explain to the guard.
As it turned out the Dundee train was delayed, and the TPE service to Manchester was held for us at Haymarket, so there was no opportunity at Haymarket to try and get my ticket.
So, I again explained to the guard on the TPE service to Manchester, and was told that wasn't a problem (a few others on the train had the same problem). Then when I got to Manchester Oxford Road I explained to the guy on the barrier and was let out without any issues, however was told Oxford Road didn't do ToD and I'd have to go to Picadilly for my tickets, which is what prompted my (rather poorly written) question about the return leg.
I had about an hour's wait after my meeting, so walked up to Picadilly and picked up my tickets from there with no issues.
What I was trying to ask, is would it be acceptable to make your return journey with no ticket as well if the advertised ToD facility at your start destination was unavailable, there was no opportunity during your journey, and no ToD facilities at your destination.
I assume in those circumstances a UFPN might be in order if you had no means to pay for a ticket onboard, but presumably you could have it cancelled on appeal as you'd paid for a valid ticket but had no means of actually getting it printed.