Of course they do, I agree.
However, it is important to realize that the software and the secure workstation that creates the files on the DTC that are transferred to the plane are the key pieces of equipment, the inner workings of which are not open to the end user at all.
The several MB to several GB of data and code transferred to the plane before each flight has many uses, both overt and covert.
The pilots are masters at using the overt data by virtue of their training and expertise. I have never doubted that. All the covert operations of the millions of lines of code and their operational effect, however, are outside their purview by design, oversight and contractual safeguards.