what exactly do you mean that the RN-42-APL BT module doesn't authenticate? I used RN-42-APL + MFi 2.0c chip for iOS authentication and it works well. However the newest firmware 5.43 has still some bug related to authentication with Android system. Previously I used BT module with firmware 5.36. Engineer from Microchip told me, that previous firmware had some bugs related to authentication which requires PIN code.
The newest firmware has been improved, but I found another one bug during my tests.
MFi chip must be connected with 2-wires to BT module. This chip uses I2C data transfer. I designed and constructed real device which was based on these components.
Finally, this module works well with iOS, authentication mode you can change with SA,x command. Please read the manual. There are 4 options: 0, 1, 2 and 4.