Is it possible to ensure audio isn't modified when playing back under Windows
Sound cards are for playing audio, not sending data.  You can't rely on an arbitrary signal not being altered by the hardware, much less the software.  For example, many sound cards have a capacitor in series with the output to filter out DC bias.  If you try to pass a DC-biased (or very low frequency) signal through such a sound card, it will be distorted.  And there's nothing you can do about it at the software level.
We have a python program which outputs specific waveforms over the audio to drive an LED, for an easy and cheap robot programming device. 
With the windows systems that we've tested everything works fine, but on some systems the waveform seems to be altered. We've used the control panel to disable any 'enhancements' for the audio output endpoint but it doesn't seem to help.
So, is it possible, using python, to instruct Windows to play audio unchanged? Or do some of the audio gurus here have another theory of what could be affecting the audio?