You can hear PL tone from my R6 and R20's headphone output. The problem is that scanner headphone audio from most manufacturers, including Icom, is too hi-fidelity. Even my Pro-106 is not immune. Usually the PL tones above 150hz or so are heard.
In fact, every scanner I have ever owned is not properly designed to roll off the bass frequencies from the headphone output starting at 300hz. This problem is exacerbated by the use of hi-fi earbuds. Thus, when using earbuds, I always hear PL tones and it is very annoying.
Hearing it all the time through your internal speaker? Something is wrong there, as the speaker is usually incapable of reproducing low frequencies, or they should be very attenuated.
One solution is to use comm-quality headsets with the proper rolloff(s) - like a Kenwood HS-5. This headset works very well since it is not hi-fidelity. Unfortunately, they are large cans - but comfortable nevertheless. As for an external, perhaps try to make a custom unit from an upper-mid-range speaker you typically find in high-end stereo speakers....
It is too bad the Icom didn't incorporate the proper low frequency rolloff in the AF-Filter option, just the highs. But don't blame them too harshly - nobody gets this right, except for commercial and perhaps some amateur radios.
AND, part of the issue to look out for is that when a scanner incorporates the FM-Broadcast band, the manufacturer usually wants hi-fidelity - much to our displeasure.
