The threshold settings only affect the decoding of the control channel. If your getting that annoying motorboat sound briefly before you hear the voice traffic on the system adjusting the threshold can help. However if your not receiving the control channel modifying the threshold will not help as it doesn't have anything to do with the actual reception.
That's wrong. The threshold setting can affect all reception. I needed a manual setting for our cities 800 P25 system. The 996XT series are horrible as they do not offer manual settings. The older T series did and perform much better as do the newer x36HP series.
I must use a manual setting of 6 or 7 to get good decodes from almost all P25 sites within my range.
Watch your decode screen sometime with it set to Auto or a Manual setting and you will clearly see fewer decode errors when it is set to the proper value in manual mode. It works for the CC as well as all voice channels in the system.
If you are simply not receiving the CC because of no or very low signal strength, then your statement would be correct but I think the OP is trying to clean up audio breaking up which may be caused by LSM. Setting a manual decode threshold can indeed help with this but it may not make things perfect.