Yesterday we reported that Google bought a link for $350,000 but explained it was a sponsorship and the intent was not to manipulate the search results.
Google's John Mueller addressed this case in a Google+ hangout this morning. "It is a weird situation", John said.
John explained that the web spam team says they try to understand the intent of the link and how common it is with the site. If it is not going to cause problems from the web spam side, and the intent is not about manipulating the search results, then in some cases Google might just discount the links and treat them as disavowed links so they won't pass and PageRank. But in this case, Google would understand there was no harm meant there.
John also noticed they changed the link to nofollow. I assume Google asked the Let's Encrypt team to nofollow it.
John said, "Looking at it, it wouldn’t have changed the ranking of the Chrome home page anyway." But John added, "If anything, we hold our web sites to a higher standard," which is why they probably took those additional steps here to nofollow the link.
The interesting part is that John said that Google may discount links "in the backend" even if they determine the link is not intended to be manipulative. They won't take action on the site in whole, but they won't count a link that is paid for, even if the intent is not to manipulate the search results.
You can listen to it at around the 52 minute mark, here is the embed at the start time:
Forum discussion at Google+.