I guess it can be confusing if you are not aware of the current situation at Chester.
I am not a regular user in this location but I do use the Merseyrail Metrocard version of Tap & Go (which lead to the start of this thread when it was being trialled).
The confusion starts with repeated automated announcements on the Train telling you you can use a Bankcard to Tap & Go at every station on Merseyrail except Chester, then on the approach to Chester another announcement is played implying that you can use a Metrocard to exit at the Barrier, but as you get off the train you are presented with a Merseyrail Validator (which you need to ignore if you are exiting the station as you tap out at the Barrier instead, I don't know what happens if you do both). If you are not exiting the station platforms, then you can use the Validators to End one Journey on Merseyrail and Start your Journey on TFW (or vice versa).
As Chester is operated by TFW, their barriers would need to tell the difference between a Merseyrail Journey and a TFW Journey as you tap your Bank card which currently they can not do, so currently they assume a TFW Journey for the purpose of the installation across their Network.
I'm sorry for causing any confusion, I am simply reporting my findings based on my Journey changing trains at this station. I hope I have not confused you any more!
BTW, I only exited through the barrier as I chose to use the facilities and the shop, neither of which were on the platform, and there was a 25 minute wait between trains. I could have used the validators instead, but I would have been confined to the platforms. And I can now confirm both T&G systems worked and I have been charged the correct amount with no missed tappings.