This is a ridiculously easy to solve problem. Timecode, click tracks, or even just recording the output of the presentation machine are all viable and simple options. Conference organizers just have to do it.
And if presentation software played the tones, anybody could record the audio at even an informal meeting and tie it to the slides. The speaker could just do it with their phone.
If the presentation software makers wanted to close the loop, they could just give you an app that records the audio, listens for the tones, uploads it to their site where you've saved your slides and automatically put it all together where anybody can see the final product.
