Correct, the only difference is that using API to set the values is doing extra work and some of it might be redundant. By manipulating SPI registers you can avoid that and do minimal ammount of configuration necessary.
Yes you can alternatively just keep reconfiguring one of the entries, it should be just as fast as switching. The difference is that to switch you need to change only 1 register, but to reconfigure the frequency you need to modify at least 2 registers (which would need to be calculated based on sampling frequency and reference clock