Currently the functional account toggle for SSL on AD accounts does not actually enable SSL for any functions that account is doing on the systems it is assigned to. It seems it is only used for testing the functional account to verify SSL connectivity is successful.
Customers enable this toggle thinking it will enable SSL for functions the account is doing, when in reality it is not. The FA configuration page should be more intuitive for the customer experience. An idea could be to add two test buttons at the bottom (one for SSL and one for non-SSL).