Re how this might apply to imposing full fare if outward wasn't completed. I know I'm tempting fate ... but for what it's worth ...... I'll have a stab.
The penalty has to be compensation for a loss sustained as a result of the breach. Not a consequential loss or indeed a missed opportunity loss or a nasty penalty to dissaude others. Trains can do a penalty for misusing a ticket but airlines cannot. It has to be a directly quantifiably loss that BA (in this case) has done all it reasonably can to minimise.
However the loss being claimed for isn't exactly a direct loss it is a a missed marketing opportunity loss. But that would be a difficult one because BA had potentially gained at the same time a seat unexpectedly just before departure that someone hadn't checked in for. They had paid for the seat but BA had also gained a marketing opportunity shortly before the flight to sell the seat again at a premium cost if they had "done their job effectively" ie had otherwise filled the rest of the plane. Could they show that they hadn't sold another seat to someone else after this pax hadn't showed?
So it might be difficult to say the penalty represents a loss of opportunity to sell a flexible ticket to the same passenger when that same passenger would have never likely bought it at the higher price in the first place and when BA might well have sold the outward seat to someone else at a high price. It is also true that flying the outward leg without the passenger has actually cost the airline less ... so a loss ist rather moot in any language.
It is in reality a potential penalty designed to encourage people to spend moeny on felxible tickets rather than compensation for a tangible loss.
Also the possibility of being declined boarding or of the possibility of a post flight fine and the precise figure it might be isn't spelt out at the time of booking making it almost certainly south of the act.
All these arguments in a court might make the penalty demand seem thinly based however some might feel about it. I think it is the combination of all of the factors that make it tough and that is why I believe is why BA have not yet allowed it to get that far.
Just an opinion ......
I don't buy the Unfair Contract Terms Act argument in the current context. I can't see such an argument can be sustained.
That said, the points you make above are very valid and this is where I feel there is great scope for argument should this issue be brought before the courts.
The argument can be braodened further, in English law a penalty is not normally enforceable. Could such a fare recalculation constitute a penalty? If so, an airline would have great difficulty enforcing such a provision in its terms of carriage.
This may well be a moot point, we don't yet know what the new rules will say or how the airlines' will change their conditions of carriage in response to the new rules.
If an airline did try to recalculate the fare in these circumstances, any such recalculation could be interpreted as a breach of the new rules and the protection that was intended to be afforded to the traveller.
Until we have the actual legal text of whatever the new rules will be, anything we discuss here is purely academic.