Since you don't want to use RDS (although it is the most appropriate tool for FM transmissions, but of course wouldn't adapt to other transmission methods), you may be able to use techniques established for audio watermarking. There is spread spectrum watermarking (SSW), which is very robust.
Search also for "audio steganography" and "realtime audio steganography". There's a potentially informative paper here that covers a number of realtime techniques, although you will have to search around to find a copy of it.
There is also steghide, which is an open source (GPL) command line tool. You may be able to adapt the algorithm there for detection in streams, although I don't know what algorithm that uses and I suspect it won't survive the trip.
Many image watermarking algorithms could theoretically be adapted for audio as well, although they may be more obvious in audio form than in image form.
A lot of the simple algorithms operate on digital data and assume no or little loss; so if you find one you'll have to test to see if the encoded data survives a trip through audio processing equipment, a transmitter, air, and a receiver. Algorithms like spread spectrum watermarking are the best bet to survive all the abuse. Start with Google searches for this and this, and related.
There is a library here (via https://stackoverflow.com/a/21269707/616460) as well; might be worth taking a look at.
There is a collection of source code for various watermarking algorithms here (presumably including SSW). Might be geared towards images.
There is a paper specifically about SSW on audio data, Spread-Spectrum Watermarking of Audio Signals.
There is a related IEEE paper, Data embedding in audio signals.
Edit: Sorry, I'm used to talking to programmers, I just realized you were looking for tools to do this.
There is a free SSW audio watermarking tool from Microsoft. I have no idea what it is capable of but probably worth checking out. See also this search.
Still, use some of the papers and search terms listed above as starting points for finding tools. I looked around a bit for hardware-based solutions but couldn't find any after a cursory search. There might be something.