As far I know not, I assume you mean:
"define the first layer temp of the materials used in the the prefix Gcode tab for each material independent"?
I know Slic3r can, because it uses unique tokens for each setting.
As said, because of the tokens in the select /deselect fields the printer is printing with the correct values of the Main / Keep warm values, but actually not benefitting of the First layer tokens when printing dual.
It's even worse actually regarding the First Layer temp used in the prefix Gcode, because, when not printing a raft, you are not sure which extruder will print first, I assume the 'support' extruder, but then it's dependent at which extruder you attached it on the Printer//extruder tab.
Actually I asked Jonathan to change the way KS uses tokens (mainly for this problem..) but it didn't seem he was willing to implement it yet. He has chosen for a structure were the Gcode fields are determing which kind of tokens are used and with which extruder (So the prefex Gcode only with the tokens of first extruder, the select Gcode only with the tokens of the new extruder, the deselect Gcode only with the tokens of the past extruder), you can't override them AFIK.
It's not super important to me, but as you say, it's not elegant either.
Bart