No, sorry, you're wrong. The toll fee remains payable at whatever amount it is set at, but regulation 7 defines the content of the PCN. The penalty charge is nothing to do with the toll fee, being payable if the fee (called "licence in the Order), has not been paid, or has been paid late. It is a penalty, pure and simple.
The toll fee is a separate debt, and is not recoverable via the PCN. There is, of course, nothing to stop the council from pointing out that the toll fee must be paid when serving a PCN, but it is not permitted on the PCN. If the council have difficulty collecting the fee there is an established legal process for its recovery.
So a non-compliant lorry would still be liable for the £100; payment of the PCN does not discharge that debt.