If you choose to call it a timing offset it's doesn't have to be thought of as a timing problem.
Let's say you have an acoustic guitar with a piezo pickup and you also have a microphone placed 6 inches from the strings.
The direct piezo signal will arrive slightly earlier than the microphone signal.
It takes the sound approximately 22 samples at a 44,100Hz sampling rate ( 0.5millisecond ) to travel the 6" distance between the strings and the microphone, so the microphone signal will be approximately 22 samples behind the direct signal.
Is 22 samples an offset or a problem? It is up to you to decide. If you were to decide to align the two sources then Channel Tools will do a great job of it.
As far as post processing and heads exploding, the OP has already mentioned that one instance of Guitar Rig placed in the effects bin can easily process left and right channels as separate sources. Many other VSTs will do this too.
You don't need to add extra SONAR buses, as has been suggested by others, to process a "side" of a two track discretely, but you can if you want to.