Is this GWR▸ 's way of atoning for their past, or apologies for the disruptions/cancellations yet to come ?
No

You are a cynic. I don't believe it's either of those reasons.
Swindon and Chippenham fares to Salisbury and stations to Southampton Central and Southampton Airport have been based on long journeys with doglegs dating back many years. Service improvements have reduced the distance people have to travel between these points. Swindon and Chippenham to West Wilts fares were reduced to match the lesser distances late in 2013, but these ones to Salisbury and the Solent area got left behind - probably because the new TransWilts service was just a trial, and
FGW▸ / GWR needed to be able to cancel it if it failed without leaving lots of debris in the timetable and fare system.
Now that the TransWilts service is permanent and part of the franchise - and indeed that First and First subsidiaries are being asked to make recommendation for the future for Swindon / Southampton traffic, it makes sense to bring the fares along the corridor into line. I expect you'll see a lot more of maps like this in the future:

Technical work and presentation at
http://twcrp.info/technical_2019 and
http://twcrp.info/presentation_2019