It really doesn't seem like the EU membership of, say, Portugal has anything to do with these problems. That organisational chart may appear overly complicated, but it's no different than any other chart for any other project of this size.

So apart from n=1 always being on the low side to draw vast conclusions, any comparison with similar projects will show that this kind of thing simply happens with complex projects. How's the F-35 these days? Or the 737-MAX?

The Airbus/Boeing comparison may actually be the most informative here, Airbus being the quintessential pan-European technology project. And if you compare them over the decades of their existence, I believe the only conclusion one can be confident in is that then national/international difference in their respective setups just doesn't matter that much.