Great Western Coffee Shop

I know that (generally speaking) a trip from A to B costs the same on the Tube as on the EL. What about if you use both to get from A to C (C not being on the EL) ? For example:- the quickest/easiest way from Paddington to Westminster now appears to be EL to Bond St, then Tube to Westminster (3 stops).  Is this a "permitted" route ?  Does one have to tap in and out of each leg of the journey ? Do you get charged for two trips or one ?
Or do you still have to go the full 9 stops on the Circle/District line to get there ?

Tap in at Paddington EL, change at Bond St to Jubilee Line, tap out at Westminster. One Zone 1 fare will be charged. No need to tap out and back in at Bond St, or indeed go up to the surface. There's Interchange between lines below ground.

It's simplest to regard the entirely new bit of the Elizabeth line (ie Paddington-Abbey Wood) as just a new Underground line for fares purposes. The Underground doesn't have permitted routes and common sense generally applies.  Delve deep into other internet forums and you will find endless discussion of exceptions, anomalies and ambiguity, but virtually nothing that will affect a typical passenger.

Other sections incidentally have differing hybrid arrangements thanks to them taking over or sharing a route with other National Rail services, coupled with legislation and agreements affecting various TfL concessions and free travel.  Some ticket validity rules date back to before the 1948 railway nationalisation, including between Liverpool Street and Stratford due indirectly to the east end of the Central line taking over some former LNER services.