If you pair program a lot you could export your Intellij settings and switch to that profile when you're on their machine. But it sounds like that only handles some of the changes that you'd need (you could move any of your Intellij related key bindings from Karabiner into Intellij to get a little closer).
Not sure IntelliJ can handle key mapping the same way as Karabiner - for example, my right option key (only the right one, not the left) is mapped to command + space. Good tip nevertheless!
Ya, fair enough... I too have some Karabiner mappings that can't be done in IntelliJ. If you're serious about it, another option could be to get a programmable keyboard so many of the keybindings are right in the keyboard and you could just plug your keyboard in to the other person's computer.