In my opinion, the manifest is the document that proves where the item shipped. In terms of a sales tax or GST audit and for goods shipped out of province or country, if you invoiced as PST GST exempt for out of jursidicition, how would you prove you actually shipped the goods out of the province or country without a manifest?
I guess you might have the shipping tracking numbers and you could input them for tracking information, but how long is this information available? And if audited, it will not be the auditor punching in the tracking numbers to prove delivery, it will be you then having to supply hard copies (which could take a considerable amount of time), and if the information is no longer available and you cannot prove the goods shipped to where stated, I am sure you can expect Finance or Rev Canada to assess PST and GST.
To me a manifest just makes sense, similar to keeping the invoices for goods purchased etc.
Jeff