From the owners manual of my 2006 passat:
“Depending on the model version, your vehicle may be equipped with one battery {under the driver’s seat} or two batteries. The second battery, if installed, is located in the luggage compartment.”
This is just one of many inaccuracies in the manual. (There is one battery and it is where you would expect it). How can a manual be written this poorly?
The real question is how come you read but did not comprehend what you were reading.
Obviously you have the model with one battery. Or since you did not state where the battery is I will assume it’s under the hood but I do not always assume it’s under the hood. Maybe you have an incorrect owners manual.
It is possible there is a typo but your post is a bit vague.
It’s not unheard of for diesels to have more than one battery. I’m not sure if the TDI models have one or two batteries though.
t’s not unheard of for diesels to have more than one battery. I’m not sure if the TDI models have one or two batteries though.
Generally, in the US they come with one battery, but I would not be at all surprised if Alaska and some Canadian areas have a second battery.
Now as to the location of the battery, All the TDI's I have seen have only one battery and it is under the hood. VW does make diesel models other than TDI's and they may have the battery elsewhere. Putting the battery into the interior of the cabin is not uncommon for cars designed for extreme cold, like the old Sunbeam IMP.Fair enough. I should have been explicit in stating that the battery is under the hood.
I don’t believe VW sold the 2006 Passat in the US with a diesel engine. At any rate there is no mention anywhere in the manual of a diesel engine.
They didn’t have any US-spec TDI models in 2006 but the European models had no fewer than four diesels availble.
More than likely trying to save money by writing one manual to cover all models and countries of this car. That and the fact that it’s written by humans and “to be human is to err.” 
I agree. Manuals, automotive or otherwise are fraught with seemingly inconsistencies intended to “service” more than one model. They are proof read for accuracy though that never guarantees they will be understandable. A few bucks off the cost of the car perhaps because one manual works.