I agree with you on the first part. However keep in mind that sometimes it's better to subdivide a problem and find better solutions for each sub-part.

The case you outlined can be subdivided into (non-dense / non-watertight) surface reconstruction followed by hole-filling on the extracted surface.

Also, the given algorithm could still be used for filling holes in the data of a single-frame of a 3D sensor, where you "only" deal with noise, but not with overlapping data "layers".