Hey there! I’m currently working on autotuning my TBS Discovery copter, and I’ve noticed that the autotune gives me a really low value for ATC_ACCEL_R_MAX. Does anyone have any ideas on what might be causing this? I’d appreciate your help! Thank you!
Noise, vibration cause that.
Improve the hardware stiffness and configure the notch filter before proceeding.
I have configured the throttle notch. I have one 5-inch racer build and 7 inch range build running ardupilot never (RPM-based notch filter using Bidirectional ESC Telemetry) never faced this issue 
Im pretty sure your Notch filter is not configured properly. Post a .bin log file.
I am facing similar issue on my 4 inch freestyle, I can t get autotune to work, tune gets worse on autotune. I suspect frame deform… but following your issue
I tried with the suggested filter setting the peaks are crushed but still, ATC_ACCEL_R_MAX is set to 4000 for the pitch axis autotune working fine but for roll 
Remove Triple notch and activate second harmonics then try again
Edit:
You will not get clean autotune with this level of vibrations. Fix vibrations then re run autotune like @Allister told you.
Fixing the issues at their source would yield even better results.
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Now autotune Yaw then again Roll and Pitch to get even better tuning.
And remove that Static notch
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You still need to fix the vibrations. They are too high.
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