Hi Kayla,
Your answer is correct that changing the out_dt will change the frequency of the output files. However, RTOUT file will be outputted once every 3 time steps if the io_config_outputs is set to 5. In your case, most probably you have the out_dt = 15 and the io_config_output= 5, which means the RTOUT is outputted every 45 minutes. If you choose a different io_confit_output (for example 0), it should output every 15 minutes.
I have not seen a file with multiple times in a single file, so cannot comment on that. But just in case keep split_output_count = 0.
Thanks!
Arezoo