HI the 3206 will not work with the Automotive software, the automotive software works with ADC212, 3423, 3223, 4223 and 4423 scopes.
The 3206 is an 8 bit scope, whilst the automotive scopes are 12 bits, which means you can analyse signals in more detail across your voltage range. 8 bits offers you 256s steps across each of your voltage ranges, whilst a 12 bit offers you 4096 steps.
You would have to take care when using the 3206 as the automotive scopes offer better protection.
A scope is a scope so it can be used in the automotive environment you just have to take into account the difference in hardware and take into account the limitations with using a non automotive scope.