The simulation did punish unneeded and useless functions by having these useless functions consume limited resources. The simulated organism dies if it runs out of resources. If you had read the paper, you would have known this.
Another bald faced lie from you. It says no such thing in the article above and that is why you cannot give a quote which says that. It is a completely a figment of your imagination. A totally made up statement with no basis in fact. Since it was completely concocted out of thin air, it is legitimate to call it a lie and not an error.
As I quoted before, the program clearly did not punish useless functions:
Some mutations that cause damage in the short term ultimately become a positive force in the genetic pedigree of a complex organism.-article-
As I have shown that is the problem with real life evolution, it does punish bad and useless functions and waste of resources - as your statement above tacitly admits. So my statement is correct and continues unrefuted - the program 'tweaked' reality in order to prove through a concocted program what it could not prove in real life.