According to a CPA friend of mine, it is not unusual for a CPA to make such concessions for clients that agree to make their schedule easier, since it then allows them to put a higher priority on high dollar clients. According to my source, VLDI saves approximately $50,000 per year by allowing this concession. But perhaps you know something about such things that this CPA does not. Perhaps you should send him an email too, and correct his understanding. I feel certain he would appreciate it, since he is telling his customers that they can file extensions without negative consequences.
However, FYI, the document you linked to has ZERO to do with this subject since it is entirely devoted to the consequences of a company MISSING a filing date, or not filing a report in a TIMELY fashion.
VLDI has not failed to file their report IN A TIMELY FASHION, since they have simply taken advantage of the law that ALLOWS them to file for an extension. And the extended date then becomes their new DUE DATE. They have not missed one of those extended due dates, and therefore any "consequences for late filers" do not apply to them.