Ah, I see where you misunderstood: In this particular context of course the 'base noise' is (using your choice of voltage) the 4V signal and the Timing reference signal is the 6V spike (triggering a positive on the leading edge and a negative on the trailing edge of the tooth in the PICO/Jag scope illustration I posted).
The main point again though is that we are just dealing with a few volts (AC) here between 'states' (ie. between tooth/no tooth/ or even double tooth..) and this can be very easily disrupted, particularly by the tooth-sensor 'air gap'; It makes more sense if/when you see a faulty P38 CKP signal in practice... I have (had ?) a photo of this -somewhere- posted up years ago on RRsnet, via a storage scope IIRC (along with the ECM illustration,) but I am not going to try to search for it on there thanks to their almost-useless 'search facility' !
If you do scope it mace take a photo ....
Not sure if your sensors work on starter motor teeth or on separate (for purpose) position sensing teeth? As I looked at it each 4v spike is signal from an individual tooth and I might assume the higher 6v spike after a position sensing gap is due to something related to magnetic flux causing a higher voltage pulse after a long period of no pulse but I'm no expert in the way these sensors work. Surely though the 4v spikes are not noise?