This is literally about a company that has a branch in the USA and another branch in another country, where it's bound by that country's laws. If the foreign entity which just so happens to be commercially linked to the one in the USA has any dealings with countries sanctioned by the US, the US branch is punished.
There was a case a few years ago where a public University in Brazil bought lab computers from Dell Brasil. Dell Brasil is a subsidiary of Dell, but it's 100% incorporated in Brazil, the computers were manufactured in Brazil, everything following Brazilian law. The computers were delivered with terms of service that prohibited them from being used for any dealings with US-sanctioned countries such as Iran and Cuba. The University was caught by surprise and questioned it, since they had many academic links with Cuban Universities, and Dell Brasil explained that.
I don't know how the whole ordeal ended. The Brazilian Federal Government got involved, I believe the Ministry of Exterior and the Ministry of Commerce and Industry both got involved and were at one point going to sue Dell Brasil. I suspect it ended with the University returning the computers and purchasing from another supplier.
The suggestion that Let's Encrypt could work around US sanctions by opening a branch in the EU falls under similar conditions, and the US branch would be liable if the EU subsidiary had dealings with US-sanctioned countries.
At least in Brazil, companies that operate there must obey local laws. What happens when those laws are in contradiction with US laws, like in the example I cited? Is Brazil supposed to cave? Is Brazil supposed to keep fining Dell Brasil until it folds? Maybe prosecute Dell Brasil's directors for actively and repeatedly disregarding the law and fines?
How does that work on a global scale?
I'll say again, this is not about a US company opening a foreign subsidiary to do things in the US that are forbidden in the US. This is about a company incorporated abroad having to follow US laws while operating wholly abroad. This is a breach of sovereignty however you look at it.