I think I am now caught up with what you are looking to do!
If you want to have a patient/provider facing application, you should be able to register and launch that application as normal. When getting tokens in the context of that application, the FinancialTransaction scopes will be unavailable.
That system account should be registered in the code Console as its own application - but within the context of your patient / provider app you can use the system account to issue FinancialTransaction requests (instead of using the system application as a separate entity as I recommended above).
Let me know if that sounds like it will work for you.