given that the input appears to be quantized,

I agree the data is quantized. It appears to be, (still waiting for confirmation from the equipment manufacturer), an artifact of the digitisation of the analogue values produced by the sensing device.

depending on what your downstream processes are supposed to do with the data,

The cleanup is required because the downstream processing -- FEM software -- interpolates between the supplied values using a cubic spline interpolation, as the simulation converges. Thus, it requires that the input data be monotonic in order that it can produce a 'single-valued cubic spline fit'.

My choice to avoid producing a "fully smoothed" fit, is because I've seen bad interactions between pre-processed fitting, and the fitting done internally by the software. These manifest themselves as interminable oscillations in the Newton-Raphson iterations resulting in extremely extended run times.

you'll get to do comparisons if/when you use a different device (or a different configuration of the current device).

The data is supplied to me; I only get one dataset per sample, but lots of (physically and chemically) different samples. I have no control over how it is produced.