The main penalty for the 2nd apron is once you're over it, your draft pick in the season 7 years later is frozen (meaning you can't trade it). And if you're over the 2nd apron in 3 out of any 5 years, your already frozen picks are automatically moved to the end of the 1st round. So teams can be over the 2nd apron for a year or two, but nobody is going to want to be over it 3 of 5 years. If you do you torpedo your franchise for a decade or more.
That's why the Nuggets are betting on so many young guys (10/18 dudes on their roster have played under 164 career regular season and playoff games); they are trying to get one last year under the 2nd apron next year because in 2 years Murray is due for a max extension (or supemax if he makes All-NBA this year). When that happens they'll have 2 more seasons before they have to start dumping guys like Porter, KCP, and Gordon to get under the apron.