I'm with you and I think a variety of companies are going to learn this in a highly expensive way over the next few years. Once your shared mental model of how the codebase works is gone it seems practically impossible to get it back. Like what would you even do if you change your mind in 3 years - sit everyone down to meticulously comb through all the AI code until they start to get how it works? Getting back to a similar level of understanding seems like it would take ages and effectively locks you into the new solution in a way that cannot be feasibly reversed.

When porting an app this way, don't functions/classes preserve the same functionality ?

Here's the critical assumption: Somebody has to know how it works, in order for it to be usable.

That's not actually true. Nobody understands everything about how an airplane works, not even the lead engineers. Nobody understands everything about how a car works, or how medical billing works, or how taxes work, or how traffic flow works, or how a CPU works, or how almost anything works. You just need to understand the broad picture and be able to find the details when necessary.