No, that wasn't what was being said.
What was said is that, in the face of "duplicate" (not "higher multiple") submissions, the editor would be unlikely to take any retaliation beyond deleting one of them, and snarling.
On the new question you've raised: In some categories (Recipes, Movies) and for some classes of sites (online e-book archives) deeplinks are common practices. For other categories (Real Estate) and types of site (directories, retailers) deeplinks are rare enough that a single deeplink will almost be enough to start an investigation for abuse.
The probability of a deeplink being accepted is also related to the distance between the categories. A site listed in a main category should basically NEVER have a deeplink in any of the direct categories. (What, never? well, maybe 1 in 20,000 sites -- it would always be inappropriate to submit such a deeplink.)
The same logic goes for "related" categories -- that is, if you can get from one category to another in a click or two, then there's almost never any reason for any single website to be listed in both. If you do submit to both, you should confidently expect one of those submittals to be rejected.
(The guidelines say, "submit to THE SINGLE best category for the site. Without some SPECIFIC reason for believing that in the SPECIFIC case multiple listings would be accepted, you should follow the general guidelines.
And again, what was said before was just emphasizing the fact that we think it's more important to give our users a comprehensive directory than it is to punish webmasters for having careless, rude, or even malicious site promoters.
