According to the service manual, only 40g (~40ml assuming the same density as water) of ink is consumed during the initial filling. It does not clearly say if that is for one head, or for both, but the latter seems way more likely in the context of the document. That's no where near $400 dollars of ink.
I'm not sure if a failed initial installment of printheads would force the same quantity of ink through both heads again during re-installation. In any case it would only be less ink wasted, not more.
I feel your pain too after experiencing lots of troubles with two iPF8400s, and dealing with the worst people I have ever encountered at Canon in my region. To be honest Canon need not compensate you on inks, but they sometimes do so out of goodwill. I second Mark's suggestion to call again and hope for better customer care.