Terminological inexactitude, and cold, hard commercial reality.
Couldn't they only tell if the link was being throttled for everyone?
Yup. Or if an ISP was being exceptionally devious, it could try prioritising CAIDA's test traffic to skew results.
It's a neat paper, but caution is needed. It uses the term 'transit' to indicate flows across network(s), ie packets in transit, rather than the more general ISP usage. So that's indicative of a paid connection vs a peering connection. Which may still end up being paid for, or at least cost. Or cost some serious $$$.
Then if 'Net Neutrality' is thrown into the mix, it can get complicated by a general lack of neutrality from various interested parties. So if a connection between ISPs is congested, who's going to pay for any upgrade? That then gets even more political if you consider content providers like Google, Netflix etc as ISPs.
But the paper shows a method and data for determining where congestion's occuring across a multi-party link. That's pretty much to be expected. Assume you're connected to an ISP that has a 10Gbps link to a peer or transit ISP, who's then connected to YouTube. The 10Gbps is full, packets get dropped. Issue is.. what happens next?
In a peering connection, ISPs might figure this is bad, and agree to increase their peering connection to 100Gbps, or Nx10Gbps via link aggregation. Congestion vanishes across that link, everyone's happy. Or, if the ISPs can't agree on commercial terms, it stays congested.
If it's a transit connection, it can be simpler. Contact your sales rep at the transit ISP and they'll quote you for an upgrade. But that can get controversial. So the transit ISP may also have YT as a customer and so your ISP may effectively be having to pay to deliver their customer's traffic. Which is where the politics and lobbying come in.
If you're a content provider, then you want to pay as little as possible for connectivity, because that cost obviously eats into your profit margins. And if your business is content streaming, like YT, Netflix etc, you're generating huge volumes of traffic.
This is where the economic arguments and lobbying come in. Problem is there's a fundamental disconnect between the flow of money between customer and content provider, and paying for the cost of delivering that traffic. So that's mostly carried by the access ISPs. They bill you for a generic Internet connection, Netflix bills you for your video service. Generally none of that Netflix sub goes towards paying any network costs for the ISP that's delivering that traffic.
Cable TV kinda manages some of those cost sharing by charging TV channels carriage fees for being on their network, as do satellite TV providers.. Which again gets political when operators and content providers can't agree on those deals.
But that's also what's behind Net Neutrality from a political/lobbying standpoint. The content providers are very much against the creation of any mechanism that may result in them having to pay more for carriage. Their position can be a bit anti-consumer, because it just means that any costs would have to be carried by users via their Internet connection charge.