When looking at a difference, you want to see positive and negative values. You are right in wanting to uncheck the option "Absolute values" to be able to observe the relative values.
Brainstorm doesn't always track correctly the contents of the source maps files, and may handle the difference of two source maps just like each of the two input files - for which most users would want to to keep the option "Absolute values" enabled.
The warning is telling you not do uncheck this option "unless you know exactly what you are doing".
In this case, you do know exactly what you are doing, therefore you can safely ignore it 