As expected, they are not able to hold the registered keeper liable for the charge* - on that basis, the keeper can appeal with something along the lines of the below:
Dear Sirs,
I have received your Parking Charge Notice (Ref: ________) for vehicle registration mark ____ ___, in which you allege that the driver has incurred a parking charge. I note from your correspondence that you are not seeking to hold me liable as the registered keeper, under Schedule 4 of the Protection of Freedoms Act 2012 ("The Act"). You have chosen not to issue a Notice to Keeper in accordance with The Act, and it is now too late for you to do so.
There is no obligation for me to name the driver and I will not be doing so. Please do not send correspondence asking me to name the driver. I am unable to help you further with this matter, and look forward to your confirmation that the charge has been cancelled. If you choose to decline this appeal, you must issue a POPLA code.
Yours,
If appealing online, be careful there are no drop down/tick boxes that cause the keeper to identify who was driving, and keep a close eye on your spam folder for their response. If they do not respond within 35 days, chase them.
*there's a link to the legislation by which companies can do this in my signature (Schedule 4 of the Protection of Freedoms Act, 2012) - as you'll see, they've made no attempt to comply with the requirements of paragraph 9, and at any rate they've sent it out too late!