All RAM can only default to a maximum value. For DDR3 it is usually DDR3-1333 CL9 or DDR3-1600 CL11.
So if you have RAM of different frequencies installed, they will still default to one of these values. Then it is up to the user to test and determine what the two kits are capable of. For example, if you had DDR3-2400 CL10 and DDR3-1866 CL8, they boot up at DDR3-1333 CL9. Next step is to test 1600, then 1866 and see what they can do. Some times they can work well, DDR3-2400 CL11 or DDR3-2133 CL9, some times they don't work at all, so it just depends on the two kits you get in hand. I don't mean the same model numbers, I mean the exact sticks you get in your hand. This is basically like the in-house testing we do to make sure each kit is matching and fully capable of the rated specs you pay for. We do this to save you the hassle, hence why we recommend purchasing complete kits rather than multiple kits where the maximum result is not guaranteed.