You can in theory use whatever frequency you want if you deal with the output of a phototransistor or photodiode yourself (though it will use the ADC heavily at that sort of frequency.
The 38kHz frequency is standard for remote controls, hence a lot of chips support it - encoding the signal onto a 38kHz carrier vastly improves sensitivity and reliability in the face of ambient light interference.
Separate frequencies should be able to interoperate if the decoder chips have narrowband filters that properly reject the other frequencies, which means reading the datasheets to find out the frequency response curves.