As above, Merseyrail don't have any real problem with accepting a limited number of e-tickets. It's only an issue if they become swamped with them and don't have the infrastructure to deal with them - particularly if it causes safety issues with throughput through the gated stations.
Merseyrail, to the best of my knowledge have never claimed not to accept
actual e-tickets and I don't think I've read or heard of any reports where they have not accepted them without any fuss at all. There is some unusual Transport for Wales carnet style product involving barcode tickets into Liverpool and throughout the Merseyrail area joining it via Bidston or Chester for years, such as:
Full details of all British rail Single, Return & Season tickets and Travelcards. Built-in Season Ticket Calculator.
www.brfares.com
The issue is all about TOD - customers think they have an e-ticket when they actually only have a collection reference. Merseyrail was trying, albeit very poorly, to communicate that difference.
A penalty fare is the correct outcome for any customer who does not print their TOD off before boarding a train at a staffed station. Credit to Merseyrail for recognising they need to address this issue through education/information campaigns, but the execution was poor.