center multiple objects + select color ignoring opacity

hello, 

in the image you can see 5 groups of dots, all dots are same size and color with 50% opacity. some of the dots are overlapping and create different colors.

1. is there a way to select the dots by the color that created? flatten transparency ruins the shapes. 
2. is there a script that can center perfectly multiple overlapping object? i want to be able to select all the dots and the overlapping ones will center perfectly.

thank you :)