When using Kontakt as a multitimbral Instr it's better to use the Controller assignments within Kontakt.
Kontakt's definition of how it's setup for automation at the instrument level is different from PLAY, Omnisphere, SampleTank, etc...
I find it easier to setup automation within Logic as a multitrimbral and specifying the number of channels (16 for Kontakt, 9 for Play, 8 for Omnisphere, etc...) and when loading the AU instrument, specify the multiout (16 stereo Kontakt, 9 stereo PLAY, 8 stereo Omnisphere) and automate on the aux outputs of each of the aux channels you create in the mixer window for the channel strip of the instrument in question.
Of course for Kontakt, there's an extra setup you need to do by creating your multi outputs for Kontakt so that Logic can see those, but you can save it as a preset for later use.
If you really need instrument specific automation, it just might be easier to create that instrument as stereo and to "instrument specific" automate knowing that you're just going to affect one loaded instrument.