Can you set a new spatial reference when merging raster tiles or should you use their existing spatial reference and then use the project raster tool. I've done it both ways and it seems to work either way but I want to know what the best practice is. Obviously if there was no risk to doing both the new raster and new spatial reference simultaneously that would save some time.
Ever step should be a conscious decision. For example, during projection of rasters in ArcGIS Pro, you need to understand and assess the affects of cell size amongst many things.
I would never recommend or advocate a methodology for "convenience" sake unless I had personally studied the ramifications of the alternatives with a variety of data sets.
So my answer, .... yes it definitely matters ... it will be up to you to decide what I exactly mean