I'm not aware of any alt origin story given the very clear and direct line between the EU and the Ventotene Manifesto. The EU's own diplomatic service tells the story the exact same way:

https://www.eeas.europa.eu/eeas/ventotene-manifesto-and-futu...

The Manifesto spread like wildfire through all the circles of the European resistance. This resulted in the founding of the movements for a European federation in several countries, the decisive Hague Congress of 1948. It resulted ultimately in the Schuman Declaration of 1950, which proposed the European Coal and Steel Community, the first step on our integration process, based on the supranational principle. Later on, in a career that included being Commissioner and Member of the European Parliament, Spinelli promoted the Treaty of the European Union of 1984, which was approved by the European Parliament. Originally rejected by the Council, it became a major influence in the writing of the Maastricht Treaty of 1992 that launched the monetary union and created the foreign and security pillar, of intergovernmental nature.

The EU was founded by communists, there's no real way around it.

Still, you are totally right that the EU is not specifically Marxist today, even though it has its origins in that world. But that doesn't mean there's no problem. Marxism is just one turn of the wheel, an iteration of the same underlying ideology that constantly shapeshifts whilst retaining its basic idealistic core. By the end of the 20th century Marxist economics was discredited. The working classes failed to rise up and revolt against their capitalist masters, turning out to be actually quite conservative and OK with capitalism. The places where "professional revolutionaries" did it for them trashed their economies and wrecked their societies.

So no longer would people who shared Marx's basic intuitions focus their energies on organizing the working classes. They adopted standard capitalist orthodoxy instead, which is why the old left tend to describe the EU as "neoliberal". And they are indeed to some extent New Liberals economically, albeit their love for capitalism is half-hearted at best. They are reluctant converts. But the same underlying intuitions about human nature didn't go away. The principles that there are big gaps between the best and worst people, that society should be united under a dictatorship of the best people, and that it's OK to bend or break the rules to get that outcome, well, unfortunately these ideas somehow did not get discredited.

And so the people who would once have been Marxists shed the idea of fully planned economies and violent revolution, replacing it with a new form of subtle diplomatic revolution. The outcomes would be the same: people are still forced into a trans-national dictatorship of "professional revolutionaries" against their will, but now the mechanisms have altered. The mechanism would be a steady accumulation of international treaties erasing differences between nations, exploiting a loophole in many countries constitutions that allows governments to sign treaties without needing the consent of representatives, and by linking all those apparently separate treaties via carefully disguised "guillotine clauses" in which an attempt to back out of one causes the immediate revocation of all of them.

This focus on subterfuge is why so many quotes from EU elites are on the theme of backroom dealings, misleading the public about what they're doing, hiding things from the public, ensuring countries can't back out when it's too late and so on. It's why the EU has a culture of intense secrecy about everything, reflected in the article this thread is about, but it's not unique to CSAM expert lists. The way von der Leyen was selected is a secret, even the way EU law is made is itself a secret:

https://euobserver.com/eu-political/136630

And often even things that are stated publicly are manipulative propaganda, which is why HN has so many posters convinced of things that aren't true, like the supposedly democratic nature of how the Commission is appointed (not true, Juncker has said in the past he vetoed any Commissioner he didn't like, which is not how it's supposed to work and not how people usually claim it works).

So the EU is fundamentally still engaged in the same old tricks. It is in some sense progress that they do it via the pen now and not the sword, but that's relatively small consolation given that the desired end state is so similar.