So jwz's use case is that he's an inbound link from a social media site, right? So Esquire is optimizing two things here: conversion rate to the downloaded app and amount of time spent on site. The first one is obvious -- people who have the app downloaded are going to spend much more time overall and are going to be more valuable; the second one is a bit trickier, since you play a balancing act between getting users to dive deeper into the publication while making sure they don't leave altogether. In this sort of case, it's pretty reasonable to assume that someone has either the data or intuition to say "Hey, if they're visiting our site from Facebook, they have a pretty big investment in trying to read the article than someone who Googled something vaguely related to the article."
(The same goes true from mobile, where audiences tend to be slower and more captive.)
So, if we understand the series of decisions that led us to such an experience, we then have to ask why were those decisions made? Clearly there's a backlash against this kind of thing -- nobody says "wow, what a great banner ad!" -- but its hard to argue against the financial straits of such a publication. Esquire doesn't have the circulation they used to, and its not a non-profit; they need to make money somehow.
Either way, its hardly fair to pin this on Esquire's web designer. Esquire's management, maybe -- or maybe the legions of people addicted to AdBlock, the legions of people who put a low -- and getting even lower -- value on content.
Now, everything is hinging on that assumption that people are vaguely competent over at Esquire. While it's entirely possible that such an assumption is invalid, I find its a more comforting one than the opposite assumption.