The blue keyframes are only for the color adjustments. If you for example want to change white balance, exposure and other tools gradually over the whole time lapse.
The Holy Grail adjustments (compensation of "jumps" introduced by changes of shutter, aperture, iso) will be done automatically in LRTimelapse 4. Those adjustments will be marked with those small orange triangles if you have them in your sequence when you use the Keyframes Wizard. The Holy Grail Wizard will then do the leveling. The orange triangles appear as 2*/3* keyframes in Lightroom, but you shouldn't touch them since they will be taken care of automatically by LRTimelapse.
So in LRT4 you have two layers of keyframes: the ones that you edit (blue, positioned as you like, by default even spaced) for your manual changes in editing and the second layer, the orange ones that will just be there to indicate where LRTimelapse will do all the magic in compensating your camera adjustments.
Make sure to have watched my latest tutorials on
http://lrtimelapse.com/tutorial - since in LRT3 this has been different.