Like Barry I think that clause 12 is intended to refer to time restrictions and indeed this is how I would interpret it. However, the phrase "the trains in which they can be used" could be interpreted as referring to an operator restriction, so I suppose with that we get into all the legal arguments about reasonable interpretations and the like, which I don't want to get into as I am not a legal proffessional. I believe there is at least one regular poster who is though.
Yorkie's quote deals with travelling on a restricted ticket and states that passengers with a restricted ticket will not be charged a penalty fare but instead will be ecessed under the conditions of carriage. However, the conditions of carriage in clause 10 states that you will either be penalty fared or sold a new ticket for travelling with the wrong company, so not excessed. Evidently this quote is intended to deal with time restrictions or route restrictions, but doesn't at all say so, so can easily be interpreted as including operator restrictions. Indeed, reading that on its own I think is how I would interpret it. Of course, this can only be used to deal with other operator tickets being used on FCC services and vice-versa.
Similarly, the penalty fares policy when dealing with ticket restrictions and routeing go on to say that a penalty fare won't be charged and an excess will be issued in line with the NRCoC, yet the NRCoC state that a new ticket or penalty fare will be issued when travelling on the wrong company's train. In terms of the routeing rule, however, I think that is irrelevent, as normally when travelling on the wrong company's train you will still be travelling on a valid, or even the same, route as the ticket was sold for.