What you see are not color information (as per vertex color). Such colors are just representations to show face groups (all faces owning the same face group ID are rendered in a certain color). E.g.: Face groups allow to select a grouped region quickly double clicking it in SELECT.
MM constructs such groups automatically doing certain operations (e.g. doing a Boolean). In case of BooleanDifference (assuming there were no face groups on both source objects): The object you subtract off (the minuend) stays white (= group zero) while the surface resulting from the object you subtract with (= the subtrahend) gets a new group ID=1 (some color). Now if there already are some groups (e.g. ID=0 and ID=1) a new ID =2 is set (a different color). So somehow the group's color is a "random" thing based on the order the groups were created.
If you do Boolean difference several times you get a new group (a different color) each time you accept the tool.
As said double clicking a group in SELECT selects a face group island. Now a face group might own several islands (split by other groups). If you want to select all islands of a group you need to hit Shift+G.
To combine different groups to a single group you need to select all groups to be joined by double click and run Modify/CreateFaceGroup (Ctrl/CMD + G)
To split off a certain region from a group: Select that region and run Modify/CreateFaceGroup (Ctrl/CMD + G)
If you don't want to see the groups but the per vertex colors of the mesh switch to MeshColorMode = VertexColor (either using the Hotbox (press and hold Space and click on the blue-gradient sphere) or via MM's Preferences)
