Now, there's obviously a problem for the homeschooled kid if he shows up to a college geology class and writes a paper that says all rocks are less than 6,000 years old. But even if the homeschooled kid flunks geology, is it really going to affect his whole academic career? What's likely is that the student, homeschooled or not, who doesn't *believe in* the ToE is just going to spit back what his prof wants to hear and go on his merry way.
He'll still have to pass a geology test, and modern geology and flood geology are, shall we say, not "parallel", to say the least.
Like I said, he's not likely to fail in his/her entire academic career if he/she fails a geology class.
Its the study habits and the commitment of the parents, not the material.