It the way I was taught in college.
Either you misunderstood or the instructor was an idiot. In my humble opinion.
Source code file names should always reflect the purpose of the file. One should not have to hunt through a directory full of files named main_x.c to find the specific file of interest.
I agree that some warning that main.pde would no longer be a valid name could have proven useful, but, I suspect that it never occurred to the team that it was necessary to warn people not to do something dumb. (Again, in my humble opinion.)