"I often hear that evolution "has no goal"."
It has no long term goal it is working to achieve (i.e., "evolving" monkeys into humans). It has a "goal" of making a species suited to its environment.
The problem with speaking of "goals" when dealing with natural processes is that you begin to think of it as having wants, need, desires, etc. -- which is what you appear to be doing -- when it doesn't and nobody claims it does.
"Nevertheless, whenever the mechanisms of mutations and natural selection are modeled in a computer program, I am able to uncover the "goal" in the program code every time."
No shit. If I use evolutionary computing techniques to help build a better widget then I want the processing power directed toward giving me a better widget, not a better doodad.
Evolution in the real world doesn't have such restraints. If a species (i.e., widget) becomes better adapted to its environment by many, many compounded changes that it becomes a new species (i.e., a doodad) then so be it. That's what it took for the species to survive. Engineers don't have that option though. If they need a better widget then the design has to be constrained to widgets and not widgets and/or doodads.
"Something is amiss.
Yes. Your understanding of both evolutionary theory and engineering. Possibly your critical thinking skills are impaired also.
"Why can't someone design a generator that spawns two random binary files. Execute both of these files and see if they communicate."
Well, the word "random" would seem to be a good indicator of why that's not likely to happen.
The Law of Large Numbers would seem to indicate that it could happen, but it would be quite a long process.
"More than likely they will crash without a proper PE header, but if so, delete them and start the process over again. Perhaps eventually, one program will produce some stdout and say, "I'm alive!", "Viva Las Vegas!", or "I want to marry the other binary. Please don't delete her (or it)."
Eventually any or all of those could happen. Eventually. If you want to wait around. Personally, I have better things to do with my time.