You say "Turbotax did calculate his taxes due on the gains and reduce his tax refund substantial". That's not supported by the numbers you provided.
Look at line 16 of form 1040. It should be 0. The reason he's not getting the LLC is because he has no tax liability to offset. I agree, TT could/should do a better job explaining that. It's shown on the form 8863 worksheet.
Although he apparently has taxable income (on line 15 of form 1040), his long term capital gains are taxed at 0% while his wage income is wiped out by his standard deduction. So, no tax liability.
