The quick answer is that there are no differences. Assuming you have Diamond 3.11 installed, you may check this default location "C:\lscc\diamond\3.11_x64\data\vmdata\database\flash". This is where the actual flash algorithms used by the programmer are located. From the file "ispVM_008.xdf", if we search the flash you are using which is "MT25QL512", you will notice that there is only one SVP file "M25L256_Algo.svp" used in all 16-pin, 8-pin, and, 24-ball packages in the dropdown.

One explanation of why there is still a dropdown even if the same algorithm is used; is that for some devices, there could be different algorithms for different package types and the scripts are created in such a way that it fits the current GUI format. The current device just happens to use the same algorithm. It's also just like a list of packages the current algorithm is guaranteed to work with.

This should not be a cause of concern. The best thing to do is to check the Flash device datasheet to see if there are indeed programming differences between the 27-Ball WLCSP and the other packages found in the package dropdown of M25QL512.