Lots of smaller files would churn the disk between creating metadata and allocating storage.
You would be amazed at home much disk seeking has to happen to create a single file (my day job is working on a commercial Unix based file system for a Fortune 100 company).
I counted the files and folders in my user/Library folder and I have 1,280,980 files (1.2 million files). That is a lot of work you are making the file system do. A single 125GB file is a lot less work.
So lets see. You have to allocate an inode (on-disk structure that keeps track of your file's metadata). Update inode with time stamps, ownership, permissions, initial file allocation. You have to find the directory file. Open the directory file. read the directory file. Find free space to add the file name. If necessary allocate more storage if no existing free space in the directory. put the file name and the inode pointer in the directory. Write the updated directory file.
Now you can start writing the file to disk. Along the way, you may need to allocate more storage. Back to the inode. look on the free block list for free storage. Remove the free blocks from the list (updating free block tracking information), add the free blocks to the inode (updating inode information). OK continue writing to the file.
The good news is that often times extending a file can be efficient if the file system looks at how large the file is when allocating and allocates proportionally large new addition. That is to day if you are creating a small file, it is unwise to pre-allocate a megabyte. But if you have a file that is already several megabytes in size, and you are adding to it, it might be a good idea to pre-allocate the next megabyte.
Some copy utilities will telegraph to the file system how big the file is going to ultimately be, and the file system can preallocate the entire file. But not all copy utilities do this, or in the case of a network attached file system, the protocol does not always allow this information to be sent back along the wire (no protocol message that says file will be this big).
So I do not think you can compare copying your user/Library folder to copying a few large movies and image files.
