I don't know Dzongsar Khyentse, much less well, so I cannot say.
Unless Dzongsar Khyentse is Punya, he did not pick out this one quote from, I assume, thousands of sentences Dzongsar has used to teach.
The afflictions give special attention to anything that can be used to wear down resolves they don't like. So Dzongsar probably has been teaching for a while and has said thousands of things, but this one quote is getting lots of attention. It's like when you give a little kid emergency money, then they want to say everything is an emergency because it means they can spend the money.
The idea of the afflictions is this, "lets ignore everything else the teacher said about keeping our vows and focus on the single time he said vows aren't the most important thing so we can disregard them".
It's like when teachers say studying is very important so students start denigrating meditation. Or when teachers say meditation is the most important thing and students start denigrating study. The afflictions like to split up and tear down aspects of the path at every opportunity.
I don't like talking about individual teachers unless I am familiar with them or their students. Let's talking about the the Buddha if we're going to talk about individual teachers.
Dvedhavitakka Sutta: Two Sorts of Thinking http://www.accesstoinsight.org/tipitaka ... .than.html
"And as I remained thus heedful, ardent, & resolute, thinking imbued with sensuality(ill will, & harmfulness one sort) arose in me. I discerned that 'Thinking imbued with sensuality has arisen in me; and that leads to my own affliction or to the affliction of others or to the affliction of both. It obstructs discernment,
promotes vexation, & does not lead to Unbinding.'"
How does it obstruct discernment? By picking out exceptions, by making big things seem small and small things seem big. Mental afflictions can also produce mental blind spots like being unable to relate to another. Mental afflictions can take over your body in a few ways, making you fall asleep during teachings or whenever you start thinking about subjects they don't like is one.