First, realize that you have not been clearly stating your question, which makes answering it very difficult. You keep switching between calling the variable in question "cluster size", "allocation unit size", and "block size". These are all actual technical terms, but they do not all necessarily mean the same thing. When you keep changing what term you use, you make it very difficult for someone to understand what you are actually trying to ask. You've also been referring to the size in question as "4096 MB", "4 MB", and "4K". 4096 MB is of course very different than 4K. Again, it makes it difficult to understand your actual question.
Next, let's clarify some terms. The parameter you are asking about (allocation unit size, see
http://en.wikipedia.org/wiki/Data_cluster) is a parameter of the file system, not of the hard drive. The "4K" hard drive parameter you are referring to is called the sector size (see
http://en.wikipedia.org/wiki/Disk_sector). These are different (albeit related) things.
Finally, let's answer your question. HD Tune is designed to measure the performance of the hard disk, not the performance of the file system. When HD Tune reads from the disk, it bypasses the file system and reads blocks directly from the disk. Therefore,
the setting you use for allocation unit size in the NTFS file system format dialog (what you posted screenshots of) will have no impact on the results you get with HD Tune. You can verify that the file system is irrelevant to HD Tune by running HD Tune on a hard disk with no file system at all. I do not know for sure if Atto works the same way, but in all likelihood it does.
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