The narrow issue is that the employer did not use the accountable plan rules to reimburse you. It doesn't really matter why. If you can persuade them to use accountable plan rules, it will mean a huge paperwork mess for them--amended W-2, amended form 941, etc. And if you can't persuade them to change, there is no way to force them, and no way to get any additional refund. The 2% itemized deduction is what you get.
The broader issue is whether you are even allowed a deduction at all. You can deduct travel and lodging expenses when you are traveling away from your tax home for temporary work. It's an interesting question, whether a college student has a tax home at all, and where it is. Your tax home might be your parent's home, or it might be college. If you don't work during term, you might have no tax home at all, meaning the expenses are not qualified under an accountable plan and also not allowable as an itemized deduction. I'm not going to investigate this for you; I suggest you leave things as they are and not submit any further questionable claims to the IRS that might prompt them to review the entire situation.
