There are other things to consider, while software locking features is one thing, in the case of the roof. If you replace the roof, it means you have to redo all the safety regulations and tests because it changes the structural integrity of the vehicle. In same way how they have to put dud cells in a battery case on lower models to not need to redo the safety

This is typical for other manufacturers. Especially in EU. Sometimes it is cheaper to manufacture the same model and lock features with software. VW would include dynamic headlights and lock their operation, keyless trunk opening, advanced cruise control, even onboard GPS. There are methods to unlock these features.
Most of the time cheapest models are 'sold' at a loss and are there only for marketing purposes. They intend for the dealer to upsell a 'better' model that has a loundry list of improvements that do not add up to the price increase.
In EU this was done mostly by including a manual gearbox on the cheapest model. If you wanted an automatic you would need to move several trims up.
The dealers I worked with told that they buy themselves base models without any add-ons. Just because this is the best value. This way you can buy a better class car than a step down class with a trim that would be 'desireable'.