The baud rate gives you a measure as to how fast, or slow a signal can change it's level. For example, if you have a 1200 baud rate, you are going to be able to send 1,2KHz sigals at the other end and you will be able to reconstruct it.
However, for a PWM you will have faster level changes as you move away from the 50% duty cycle. For example, at 75% duty cycle, the levels will change from low to high to low twice as fast than a 50% duty cycle signal.
This means that you will need to do a few sums to see which will be the smallest duty cycle your system will handle. Example: suppose you have 1200 baud radio, and a 600Hz PWM frequency carrier. If you put a 25% duty cycle, you will have a signal pulse of about 41us.
Now at 1200bauds the signal changes at about 42us. So in theory anything that changes faster than that will not change it's level. So now we can see that anything below a 25% duty cycle or above 75% duty cycle will not be seen as a change.
To transmit a signal like that has it's limitations. Do your maths taking the baud rate and pwm carrier frequency and see if it is ok for your application.
If it is not ok, you will have to code it and generate the PWM locally with another arduino.
Hope this helps.