I would argue that decompiling the official program to see what tricks they used would eliminate the Critical Flaw, and enable the programmer to complete it in 5x8 with a very high likelyhood. It is, of course, contrary to the EULA to decompile and learn their secrets, but that's not your problem if you're buying the discount program off the grey market.
The problem doesn't seem to me to be one of just coding for a series of functions within one machine, it's integrating multiple systems and their inputs and outputs via the Model x. computer on board any particular vessel.
I've seen some large applications blow out significantly in time, cost and manpower input due to system integration problems. I reckon that the same would be the issue on board a starship. Using the program would be business as usual for a character with prior experience and knowledge from the military or merchant services, but there'd be a lot fewer individuals with experience writing the software for all the systems and then integrating them together. As mentioned, that could be a job for VI machines.