Out of interest, how do you know that? When I put the route in on GWR's site it routes me through Hayes & Harlington, not Paddington.
The way that a fare is priced, and the default itineraries that appear on journey planners, are not necessarily the same.
Fares are priced based on their validity. The fact that the fare has a Maltese cross (✠ symbol) is the giveaway here: this signifies that it is valid on Underground services to cross London and thus it must be valid (and intended to be valid) via London. Since the fares aren't routed to exclude the use of the Heathrow Express, they are valid on it and that explains the high pricing.
Default itineraries are generated based on the fastest available route, or the route with the fewest changes. Since trains now run more frequently between Heathrow and Hayes & Harlington (and Hayes & Harlington and Reading) than before the full Elizabeth line timetable was introduced, this means this changing at Hayes & Harlington is now often the fastest route. In the past travelling via Paddington would often have been quicker, which explains why the fares were created and priced the way they are.
The thing is, railways are still regulated. If it were the local corner shop they would be free to act as they see fit.
Clearly there are differences, but railways are mainly regulated in a safety context. There is much less regulation in other contexts, and certainly no duty to act in a fair manner to customers as is the case in the financial sector, for example. Even the minimal non-safety regulation that does exist, such as the Passenger Rights and Obligations Regulation (PRO), is hardly ever enforced.
But rail companies have to act in the public interest
Unfortunately they don't - they are merely private companies acting as contractors to the government. Even the government isn't legally obliged to act in the public interest, and indeed in many ways it could be said that it isn't doing so in the context of railways and public transport.
There are also lots of facets to the public interest. Some might argue it's in the public interest for fares to be as high as possible (even if this reduces in fewer people travelling by rail) if this is what maximises revenue and thus minimises taxpayer subsidy. I'd certainly disagree with that - but it's not as simple as saying that the public interest necessarily dictates one course of action.
if it can be shown they are charging punitive, deceptive or discriminatory pricing
Whilst I'll readily agree that the pricing to Wokingham is punitive in the context of the most likely route for journeys, it's not deceptive, nor can I see how it's discriminating against anyone in particular (let alone a protected characteristic, if that's what you're alluding to?).
, they can be made to change them. As you say, it's a long shot GWR will respond positively of their own volition, but with a bit of exposure from, say, Which? magazine, that might change quite quickly.
They can only be made to change it through political pressure, but this seems such a niche issue that I would be very surprised if you manage to attract any attention to it.
It's a very noble issue to campaign about but I can't help feeling you will have more success if you focus on the fares being unreasonable, rather than an (unfounded) allegation of illegality.