Yes, it seems that in that one case that Chester Magistrates took a strangely unrepresentative view of the matter compared to other Courts, who have been much more robust in recognising the offence and dealing firmly with this anti-social activity.
Yes, and of course the papers love the "loony prosecution of educated girl" angle, hence the (sole) years old article.
There are only two things that anyone need note about that particular episode, and combine them:
1) That it happened in 2007, 8 years ago, and such prosecutions haven't been in the papers since.
2) That the OP's friend has in 2015 had his details taken, with information on Merseyrail's website indicating quite clearly that prosecution does happen.
If 2007 was the watershed that some seem to be claiming, then the OP wouldn't be posting here now.
Regards the byelaw mentioned earlier, as someone who regularly travels on various cities transport systems, I can categorically state that "feet on seats" certainly interferes with my comfort and convenience. I get on a train in Birmingham and the seats can be absolutely filthy and worn, especially the edges of them. Once you notice it, and think about it, and consider the various inevitable components of that encrustation, and notice the various yoofs sat around with their feet up, both shoes on and off, then it makes you reticent to sit down. It certainly ticks me off when I do sit down and one of them gets on, sits on one of the opposite seats and puts their feet up on the seat next to me. I get on a train in Liverpool and the seats are seats. Clean and comfortable, sit down, travel. As it should be.
No one's got anything to complain about in regards to this enforcement.