With the cutout it lines up, moves forward off the crossmember and rotates downward away from the floor pan so there's lots of clearance. Maybe the crew cab has a different shape to the floor pan.
In my opinion, the newest NVG-261 & 263 transfer cases fit the GMT-400 (90s body style) floor pans as well as the NP-241 (which came stock in the 90s trucks) does.

When the Duramax, Allison and the transfer cases were designed, all GM Powertrain had to work with for package design was the GMT-400 trucks. GM produced at least a dozen test mules using the GMT-400 in the late 90s. It's no coincidence that items like the radiator (bolts right in), firewall shape & clearance for the rear mounted turbo and exhaust system, and even transfer case all match the GMT-400. The divot in the Duramax driver's side exhaust manifold is a perfect fit for the GMT-400 steering shaft. That divot isn't necessary in the GMT-800 trucks.

The Allison and the transfer case are installed in the truck as separate pieces. When doing this, I can't imagine there being a clearance problem, even without a body lift. Even more room with.

I've read where Eric Merchant gmdieseltech.com has a fix for the transfer case issue.

Jim