I am uncertain as to where I would get a good explanation for my problem. I designed a board that uses the AM3358 and I did not use the pin mux tool to guarantee that I would be using a "proper" pin mux. I just grabbed the proper peripheral pin as stated from the datasheet as I assumed that any combination could be used. I was told by the programmer for the board that the use of the pins that I chose were incorrect because it violated the IO Sets (I used a tx pin from say IO_Set 3 and an rx pin from IO_Set 5 for UART - just as an example).
Of which I am not certain, if I happened to have violated the IO Sets, what is the real consequence? Does the TI chip actually prevent the functions from working if it is in violation of the sets? I am only familiar with the peripheral functions of the NXP, STM, and Atmel chips. Those chips allow for any combination that can be conceived.