Over the range microwave venting
I would find a boot that covers the cabinet opening and install that, then see where you stand. A bit of flex duct may be a good solution (the semi-rigid kind, not the cheap foil junk), but a side-offset boot may line up perfectly. This one looks like what I have in mind, though the offset may be an illusion:

Image courtesy of Home Depot
Be aware that such a boot should slip over the flange on the microwave, eliminating contact between the exhaust and the wood of the cabinet.