This will help to protect against BGP Hijacking attacks.
During a BGP hijacking attack, the attacker can re-route the traffic though its own servers, allowing him to perform a MITM attack.
This allows him to create malicious responses to the challenges, which will be accepted by Let's Encrypt, and a certificate will be issued to the wrong person because of this.
Because of the lack of effort to fix BGP despite attacks being committed since a long time, Let's Encrypt plans to test a solution named Multi-Perspective Validation.
Using multiple independent networks to perform the validation will require an attacker to hijack more routes than before, thus raising the cost of a successful attack.