I'm planning to do a journey from Reading to West Hampstead Thameslink on a forthcoming Sunday.
Just to clarify, are you wanting to travel via central London to the Thameslink station? If so, you won't be able to buy a Sunday Out ticket - Sunday Out fares are only available from Reading with the route "via Richmond", requiring you to travel on SWR via Richmond to the Overground station adjacent to the Thameslink station.
1) Despite a routing guide of National Rail services, am I still allowed to use London Underground to get from Paddington to London St Pancras?
Yes, if you buy a walk-up ticket then the itinerary you are given isn't mandatory to follow. It is just a suggestion of a valid journey.
Tickets with a cross-London Maltese Cross marker (✠ or similar) are valid on the Underground, DLR, Elizabeth line or Thameslink on any reasonable route between the permitted interchange stations (see the list half-way down
this page).
2) is it actually quicker to get from London Paddington to St Pancras by London Underground, or Elizabeth Line/Thameslink.
If you are already on the Elizabeth line and intend to change to Thameslink, then it would almost always be quicker to travel via Farringdon as the interchange there is very easy - you want to be at the very rear of the Elizabeth line train, when heading east, for the quickest change.
If you are taking GWR from Reading, it probably still favours the Elizabeth line as the interchange at Paddington from the "trainshed" to the Elizabeth line platforms is fairly quick and easy. You want to be at the very front of the train (but obviously not in first class unless you upgrade) for the quickest exit.
Bear in mind that the ticket will likely be issued to "West Hampstead Stations" and that, in combination with the Maltese Cross, this means it's valid to use the Jubilee line to West Hampstead (the Underground station). The interchange between the Elizabeth and Jubilee lines at Bond Street isn't great, requiring an escalator up, a fair walk, and then a long escalator down, but it's still likely to be the quickest way of making the journey overall.
Alternatively you could change at Paddington onto the Bakerloo or Sub-Surface (H&C/Circle) lines and then again at Baker Street for the Jubilee line.
3) Am I allowed to break the journey at London St Pancras, if I use Elizabeth Line and Thameslink? The reason I ask this is previously I did a journey via Farringdon, however when I broke the journey there to obtain breakfast, the barriers would not let me exit.
Yes, break of journey is permitted on the vast majority of walk-up fares, including those between Reading and West Hampstead Stations. However, if you use the Underground or DLR for a cross-London transfer then you cannot recommence your transfer with the same ticket, and would have to pay separately to continue the transfer. However, it would still be valid to continue on National Rail services once you reach the relevant interchange station.
Unfortunately, ticket barriers aren't always set up correctly to allow break of journey, so you may need to speak to staff to be let through. The Elizabeth line isn't an Underground line, and so break of journey is technically allowed at Elizabeth line stations. However, TfL's policy is to treat it as an Underground line for ticketing purposes in its 'core' section (between Paddington and Abbey Wood/Stratford), so good luck trying to recommence your cross-London transfer once broken...
