As noted in the article.
"As in past years, the accountants also noted that Kelly “is permitted to receive compensation from external sources with prior written approval from the university.” Since the university is not a party to those agreements —- for example, between Kelly and Under Armour — and the coach doesn’t provide any services to the university because of those agreements, they don’t have to be included in this document."
Kelly is easily in the top ten of all college head coaches re: what he earns as head coach at ND. Because ND is a private institution, it is doesn't have the reporting requirements that public institutions typically have. Therefore, the total sum of what Kelly makes is typically shrouded in mist and fog. While I don't know specifically what Kelly makes in total, I once learned (since this is my career field of professional expertise) what one of ND's head coaches was making and his reported salary was a fraction of his total compensation.
Rest assured that Kelly is not underpaid in relation to his peers. While coaching pay may have lagged at one time at ND, I pretty much know that in the last 15 years, pay is not a cause of coaching turnover at ND nor does it really limit the guys ND wants to hire at the assistant coaching level. It has already been published that ND offered Mike Elko 1.8M to be DC when A & M was after him. Do you think Kelly was making only 1.86M? when they offered nearly the same for his DC?