What the three groups mean
Formalities are checked before any facts are read. A missing signature, jurat or provision, or an unaddressed failure code, gets a Letter 1948-C on a current-year case (30 days to cure, and the IRM allows only one suspense) or a closed file on a reconsideration (IRM 4.19.25.8(3) to (4), 4.19.25.13, 4.19.25.17.1.3).
Substance is the two-part reasonable-cause test as the examiner scores it: did you react timely, did you prevent recurrence, and is there a mitigating factor or an event beyond your control from the list the examiner is given. If you are silent on prevention, the examiner pulls your next year's filing and answers for you (IRM 4.19.25.8(6) to (7)).
Denied on sight are the things the IRM's decision tables resolve without judgment: annual solicitations by electronic means ("Deny the request for relief. Assess the penalty."), a plain postage receipt as proof of filing, First Time Abate, and an 8821 where a 2848 is required.