The power source loads the coil the signal tells the coil when to fire. The stored energy runs up the wire to the spark plug and fires the plug. About a hundred years ago someone figured out which direction the coil would send the pulse. If they didn't, starting your car would be a lot more exciting. Now, with these cdi ignitions if they are fired without a looped ground the signal gets zapped and blows the pickup sensor instantly and shuts down. Either someone forgot how to wire the coils for polarity or they figured the system would shut down imediatly should it go haywire.
So far there's no reason stray signals should run back to the supply side battery.
About the only long term problem I see is not having a battery with enough oomph to send a strong steady feed of power to the cdi. Where the high frequency bumps the coil/s are drawing from the battery might set the rx to see the power fluxuate at a frequency that disrupts it's opperation.