There are a couple assumptions here - and knowing the 'back story' can help you read between the lines.
The first has to do with the requirements for a 3R enclosure. Contrary to popular belief, these enclosures ARE allowed to have minor amounts of water enter them during the test. It's only required that the water not pool high enough to reach the 'hot' parts.
Therefore, strictly speaking, there's no 'rule' against pipes entering anywhere on the sides. There is, however, a LISTING standard that says 'no FACTORY ko's above the 'hot parts.' This is because of a belief that pre-punched ko's are likely to leak, or be pushed in by playful gremilins.
As for the quote from the UL "White Book:" the speaker was addressing the different types of pipe threads, and where they are used. That is, the difference between the straight thread on EMT fittings and the tapered thread on RMC fittings. What the speaker is saying is that the sealing locknuts are intended for use on the tapered threads - in fact, they probably won't fit on EMT fittings at all. They certainly won't go on very far.
I believe the inspector is trying to do a good job, but that he's reading too much into things.