DART are permitted to recover the RUC, it says so in the Regs and is repeated in their Charging Order.
But neither the regs nor the order permit recovery as if it were a penalty.
IMO, a DART PCN sails close to the wind but does not, other than by implication, require the RUC to be paid. The reference to a CC omits any suggestion that the RUC is recoverable. However, as shown in another current thread the CC itself goes too far IMO by stating that if 'You do not pay' - without any qualification and which could only reasonably be interpreted as referring to Total to Pay which includes the RUC- then 'you will get a court order demanding payment'.
This thread has similarities. The PCN clearly separates the penalty from the RUC and it could be argued by them that this is simply a statement of what's owed i.e. the penalty as a penalty charge and the RUC generally as permitted under the order. Perhaps the OP could find out what is demanded on the authority's website payment page.
In the Caroline Sheppard decsion the authority at that time went so far as to defend its position but whether this remains the same today I don't know.
OP, have you actually sent your appeal? I ask because 'It therefore follows that penalty and user charge fees are not due. I trust you will cancel the referenced PCNs.' Is not a statement of the law as I understand it. The penalty is owing because you failed to pay the RUC in time. It is the RUC which in fairness cannot be owing because you paid it* prior to the PCN being issued.
*- does your receipt show clearly that your payments were in respect of specified crossings? We wouldn't know, we haven't seen them.