In some ways I'm a bit surprised that the through ticket says to transfer by tube, unless it is a day when the Elizabeth Line is closed for engineering work.
Or maybe this is a misunderstanding of the debate of 'when it is a tube line, a tube line?' (the answer concerns the Elizabeth Line).
A test booking shows that the indicated itinerary is Thameslink to Faringdon, then Elizabeth Line to Paddington, in which case QR codes will work the gates at Paddington, and I don't think you go through a gateline at Faringdon. But if you do the QR codes will work as it is National Rail to National Rail.
The maltese cross on a paper ticket is there as a manual indicator to ticket examiners of the validity of the ticket, in case the magnetic coding fails.
In overall terms this is why if you buy a ticket involving cross London travel on the tube it normally has to be collected in paper form from a machine prior to travel. Looking for tomorrow an Advance Ticket from Gatwick to Bath is only £1 more than one from Paddington to Bath, on the same train from Paddington.
But a flexible ticket on doing some checks is a lot cheaper bought as Gatwick to Paddington (£24.30) + Paddington to Bath (£43.80) compared to £89.90 as a through ticket (Super Off Peak Single).
Even cheaper is to do Gatwick to Paddington contactless for £13.50.
Another cheaper way to do the journey, on walk up flexible fares, is to take the Gatwick to Reading train (direct, not through London), change at Reading for Bath.- £43.10 Super Off Peak Single (bought split ticket Gatwick to Reigate/Reigate to Bath, stay on the train at Reigate ). By contrast the cheapest Advance (train specific) fare I can see for tomorrow via London is £41.50.
Bought as an Off Peak Single Gatwick to Bath (no split) Gatwick to Bath via Reading is £77.10- so a huge saving from the split.
So the non London route seems to be the better route in terms of flexibility vs cost