Users may still able to edit a scheduled program and add membership restrictions even if it is already part of a Group Sales flat-rate scale. This seems like incorrect behavior since you are prohibited from selecting a member restricted program when adding a new flat-rate scale.
Users are still unable to sell tickets, and therefore are not able to use this as a workaround to circumvent member only event restrictions.
Steps to Duplicate
Go to Tickets > Group Sales Setup > Flat Rate Pricing
Add a new rate scale
Enter a Name
Under the Application Details section, search for and select a Scheduled Program that has no membership restrictions
Enter Percent = 100% and click Add
Under Prices, enter a dollar amount
Now, go to Tickets > Program Search
Search for and open the Scheduled Program
Edit the program
Enter some membership restrictions and Save. No error occurs