The alignment needed to be corrected because of the aftermarket parts, not because the factory alignment was not within specifications. Glad yours had good fit and finish, but I’m referring more to the long term durability of their painted components and materials, which are not subject to any OEM standards.
As far as warranty, anything that Tuscany/Shelby has modified is not covered by Ford. That includes the seats, all aftermarket or repainted body panels, all aftermarket or modified suspension components, the wheels and tires, power running boards, etc.
The powertrain warranty is also impacted, because Tuscany installs a tune to increase horsepower to 525 and torque to 610 lb-ft. Therefore any failure that is be attributable to the tuning or increased power output is non-warrantable. That ranges from broken piston ring lands to differential failure. This is the reason that Shelby/Tuscany includes a separate 3yr/36k warranty on their products. However, if you experienced a powertrain related failure at 40k, you’d be out of luck since the Shelby warranty would be expired and Ford doesn’t cover their modifications under the factory 5yr/60k powertrain warranty.
OASIS will not show anything abnormal because Ford doesn’t know what’s been done to the truck. All they know is it rolled out of Dearborn truck as a stock Raptor and was shipped to Shelby/Tuscany.