Your drawer height might matter, but you should have plenty of room. I have a single drawer on one side that's ~11" tall and IIRC I have ~35" above the drawer, maybe more. The trunk is >40" deep and the hatch itself is >48" wide where it meets the tailgate so you should be fine.
If you don't want to deal with a kennel and/or if you need a cargo divider, you might consider getting the center divider, 3rd row attic, and 3rd row divider from Kaon. I do that and my dog stays contained to the driver's side drawer area. (cooler fits nicely on the passenger's side). The height of the center divider is adjustable by about 6", and they have a few different sizes if your drawer height varies too much. Reference pic.
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