You have read it right grahame. Poorly worded and implemented routeing restriction on the cheaper 'via Swindon' standard class fares.
The intention of the restriction is, I suspect, to route people through Swindon, but not via Bath Spa. It seems the booking engines aren't applying that.
However, even if that is the intention then, as pointed out, one goes 'via Swindon' whether they leave Melksham north or southbound.
With the anomaly now highlighted publicly, one can expect
GWR▸ to look to protect their Bath - Reading/London revenue by changing the restriction wording and tightening up the booking engine implementation. 'Not via Trwbrdge' perhaps. Leaving the 'Any Permitted' valid via all three routes allowed by the Routeing Guide - Trowbridge/Bath, Trowbridge/Westbury, and Swindon.
It's not just the Super Off Peak that has savings. The Anytime Return from Melksham - Paddington 'via Swindon' Is £171.60. That too can be used via Bath Spa. Saving Bath - Paddington passengers over £25 (£196.80).
Now take a look at the 1st Class fares. The price differential is reversed. 'Via Swindon' is more expensive than 'Any Permitted'.
A complete dog's dinner of fares choices.