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merging vs. mosaicking

Does anyone know the differences and implications of merging projects within Pix4D versus simply mosaicking them in ArcGIS or QGIS or R?  Would the Pix4D merge result in a unified cross-calibrated output vs. maybe mosaicking would result in not being able to safely compare the output values from one tile to the next (i.e. be able to use both tiles in same statistical analysis), comparing apples to oranges? 

If merging is superior to mosaicking, is there 3rd party software than can handle more images than Pix4D?  We have a 1000 Ha site that we would like a to generate a single NDVI raster, a single DSM, and a single DTM/DEM for. 

And if mosaicking adjacent projects is just as good as merging, what software to people recommend for mosaicking and why? 

Thanks!

If you have time , lets have a quick chat reference your questions.