Embankment is classified as interchange with Charing Cross, Temple isn't.
See
http://www.nationalrail.co.uk/times_fares/ticket_types/46587.aspx for the full list of stations.
(I was surprised to see that they are not all zone 1 stations. Stratford is in zone 3.)
A national rail ticket marked with a Maltese cross entitles you to one cross London journey. In practice I think it means that your ticket will open an entrance gate at any one of the stations on the list and an exit gate at any one of the stations on the list. As I understand it
TfL» is being paid a fixed amount for providing a single tube journey and so long as you take no more than a single tube journey between any of those stations they are not really concerned about enforcing complex routing rules (and their automatic gates are not sophisticated enough to do so anyway).
You can break a cross London journey (although you may need to be let out the station manually rather than use an automatic gate), but you are not permitted to re-join after breaking a journey. So with a Chippenham to Stansted national rail ticket you could use the ticket to travel Lancaster Gate to Oxford Circus (Lancaster gate is on the list above and within walking distance from Paddington) and enjoy some fine dining at the Oxford Circus Angus Steak House. But you would need to buy a new tube ticket to travel Oxford Circus to Liverpool Street.
