[cnvogel]

I think it's foolish to assume to have the magic tool that will instantly give you a meaningful probability distribution that can statistically reproduce arbitrary datasets. Once you've choosen a certain bandwidth (by fixed binning, or choosing a kernel) you've lost the ability to resolve structure finer than this, and you cannot quantify parameters (e.g. the macroscopic view) much larger than that.

But of course, playing around with these parameters will hopefully give you a nice plot, insight into the problem and allow you to propose a proper model describing your data. Then you can fit this model to your data and extract the model parameters more precisely.

And when the distribution width of the toplogical features match your kernel sizes, of course, this PDF will look almost identical as the density plots.