The Form 1098-T has nothing to do with the Form 1042-S. They are unrelated. The 1042-S is income, the 1098-T is for educational tax credits. You could be a US citizen, and have your employer pay for your education (Which would be taxable and put in your Form W-2) and still get a Form 1098-T and be able to take a tax credit for the education expense.
As I said, your RA position is what enables you to get the room and board for free. This is under the Internal Revenue Code, and NOT through any tax treaty. This is the same for you as it is for a US citizen. So stop worrying! It is a nontaxable fringe benefit under Internal Revenue Code §119.
IRC §119(a) - Meals and lodging furnished to employee, his spouse, and his dependents, pursuant to employment
There shall be excluded from gross income of an employee the value of any meals or lodging furnished to him, his spouse, or any of his dependents by or on behalf of his employer for the convenience of the employer, but only if-
(1) in the case of meals, the meals are furnished on the business premises of the employer, or
(2) in the case of lodging, the employee is required to accept such lodging on the business premises of his employer as a condition of his employment.
In English, this code section basically states that if your employer provides you with free housing, you can exclude the housing value from your gross income if your employer satisfies certain requirements. The lodging must always be on the employer's premises, acceptance of the on-site housing is a condition of your employment and there must be a business reason for providing the lodging, which means the housing is solely for the convenience of your employer and not yours. In your case, you are living in the dorms (your employer's premises), you have to live there as a condition of employment (how can you be an RA and not live on the floor?) and the housing is for the employer's benefit (having you as an RA helps your employer maintain the dorm safety/living environment). Yoru meals are in the cafeteria (your employer's).
So the value of your room and board are NOT income to you, regardless of you are a resident alien or a nonresident alien or a US citizen.
So stop worrying! You are fine!