I see how that would appear to be a contradiction. However, your takeaway from the Yale Law Journal link is incomplete.

The Yale article argues that Amazon has avoided anti-trust scrutiny because most anti-trust regulators are laser-focused on price and output (is Amazon fixing artificially high prices? Is Amazon artificially limiting output?), and this approach misses the ways in which Amazon limits competition (mainly predatory under-pricing and vertical integration). The article goes on to suggest that by ignoring these, antitrust regulators are "overlooking the structural weakening of competition until it becomes difficult to address effectively, an approach that undermines consumer welfare."

You're right that the article does talk about practices that aren't mentioned in the complaint, like predatory under-pricing.

However, it also discusses the ways in which Amazon uses vertical integration to create barriers and reduce competition. Here I quote from the article:

>Amazon is positioned to use its dominance across online retail and delivery in ways that involve tying, are exclusionary, and create entry barriers. That is, Amazon’s distortion of the delivery sector in turn creates anticompetitive challenges in the retail sector. For example, sellers who use FBA have a better chance of being listed higher in Amazon search results than those who do not, which means Amazon is tying the outcomes it generates for sellers using its retail platform to whether they also use its delivery business. Amazon is also positioned to use its logistics infrastructure to deliver its own retail goods faster than those of independent sellers that use its platform and fulfillment service—a form of discrimination that exemplifies traditional concerns about vertical integration.

>The clearest example of how the company leverages its power across online businesses is Amazon Marketplace, where third-party retailers sell their wares. Since Amazon commands a large share of e-commerce traffic, many smaller merchants find it necessary to use its site to draw buyers.These sellers list their goods on Amazon’s platform and the company collects fees ranging from 6% to 50% of their sales from them.

These quotes map pretty cleanly onto two of the complaint's allegations:

>Conditioning sellers’ ability to obtain “Prime” eligibility for their products—a virtual necessity for doing business on Amazon—on sellers using Amazon’s costly fulfillment service, which has made it substantially more expensive for sellers on Amazon to also offer their products on other platforms. This unlawful coercion has in turn limited competitors’ ability to effectively compete against Amazon.

>Charging costly fees on the hundreds of thousands of sellers that currently have no choice but to rely on Amazon to stay in business. These fees range from a monthly fee sellers must pay for each item sold, to advertising fees that have become virtually necessary for sellers to do business. Combined, all of these fees force many sellers to pay close to 50% of their total revenues to Amazon. These fees harm not only sellers but also shoppers, who pay increased prices for thousands of products sold on or off Amazon.

At the end of the day, Amazon is a very big company that does a lot of different things at the same time. It could be under-pricing ebooks and overcharging FBA sellers at the same time.

The point of the Yale Law School article is that anti-trust law ignores anti-competitive practices until they significantly distort prices across the company's largest market, but that these practices have a chilling effect on competition far before that point. Khan argues that anti-trust regulators should go after companies using these practices before they cement market leadership and fully edge out competitors.

>On the Chicago School’s [(the pre-existing paradigm's)] account, Amazon’s vertical integration would only be harmful if and when it chooses to use its dominance in delivery and retail to hike fees to consumers. Amazon has already raised Prime prices. But antitrust enforcers should be equally concerned about the fact that Amazon increasingly controls the infrastructure of online commerce—and the ways in which it is harnessing this dominance to expand and advantage its new business ventures.

This is exactly what Khan's FTC is doing now.