Why does Mac OS overwrite whole folders rather than merging their contents?
Merge two folders with the same name

If you have two folders with identical names at two different locations, you can merge them into a single folder.

Press and hold the Option key, then drag one folder to the location that contains a folder with the same name. In the dialog that appears, click Merge.

The Merge option appears only if one of the folders contains items that are not in the other folder. If the folders contain different versions of identically named files, the only options are Stop or Replace.