My kids want to use Unity3D for a science project

From an excellent 6th grade science teacher comes this question. My answer is beneath. I have a couple guys in 6th grade who are dead set on doing a science fair project involving video games. Both guys want to use a program called Unity 3D. 

How in the hell do I turn this into a project with an authentic research question such as "What affect does __________ have on _________?" 

If you have any suggestions or could help me point these kids in a different direction, I would be most appreciative. This is tricky to get right. In a nutshell, you have to be much more strict about the instructional design than with other activities your kids might want to try. The problem is sadly universal. The boys will absolutely light up about this project. They will go full-nuclear in their enthusiasm, energy, and time with this. But at the end, there is a very good chance they will not meet your learning goals. 

They will tell you, brimming with excitement, "look! we made this guy's arm move, and we put in the radioactive monsters that blah blah blah". And you will ask, "have you met these learning goals? And they will pause. And there will be this uncomfortable silence, and then they will say "look at the tank we built!". This is the same thing when kids build a powerpoint presentation that is all fluff, and no content. So if you are willing to hammer them with oversight (and I mean a daily check-in against an obnoxiously clear rubric), then I say go for it. 

Also, please know this project will take longer than other projects because the kids are going to want to do everything, all at once. One last thing: If your kids do choose to use this learning tool, and they manage to model their science project as a simulation, it will be a very powerful learning experience. I can't think of a better way to learn than to create a simulation or a digital representation of an idea. I'm curious how you will proceed.