An option similar to Inquiry > Duplicate Points - but in this idea, average the selection based on X, Y, Z tolerances and the averaged points to be assigned into a new layer and retain (not delete) the other close proximity points within their respective layers. The new layer will show the averaged X, Y, Z points. The window/all selection of the points will use an algorithm to calculate the average within the tolerances applied.
In addition to this (from a customer) - Separate function from Duplicate Points and with the ability to remove outliers and checking residuals