"Being in SF" is a silly excuse. There is no reason for them to be in SF.
EDIT: Source: I work on a fully remote team (>50 people) with teammates around the world who are high caliber people.
It was a response to the claim that "there's no reason for them to be in SF" which is an odd assertion.
The point is that comparing an actual team with a purely hypothetical one is really just an exercise in imagination. These people exist, are competent, happen to live in San Francisco, and this organization has built a compelling product paying them what is likely lower than what they would earn at other employers in their region.
As I understand it nothing is preventing another service from emerging that competes with Let's Encrypt and has a better cost structure. It may also be reasonable to refrain from donating to / funding Let's Encrypt if you feel that they are poorly managing their finances, but even that to is more productive than simply stating "this team should not be in SF".
The reality is everyone is playing armchair quarterback/back seat driver/whatever and telling LE about that they COULD do. As if somehow LE was dedicated to overspending. As if they didn't scour the earth to find the people and save 25-50%.
Building a good team is hard. Building a good distributed team is harder. That they exist is just as much luck as anything else.
It's hard work. It's challenging work. It's been screwed up a few times, yes. But it's not the sort of thing that's so hard that only five people in the world can do it correctly or something, though.