From Sebastians site; "The last line of the song isn't "fried chicken". After that line the choir says "vision vision vision..." and then Brian says again "God works in mysterious ways ... mysterious ways". So that is the last line of the track."
the part from GVH2 is a whole different take!
And in case you didn't noticed, 'mysterious ways' is sang 2 times
"God works in mysterious ways....mysterious ways" slowed down and distorted, And there are a lot of reversed voices aswell during the intro
Moreover the fact Freddie says 'God works in mysterious ways' in the documentary doesn't mean that it was the take used in the record. Just like Brian's synths, they could be programmed in the final edit