True, that ended up in the Constitution, but it was by no means seen by all the delegates as the best way to elect the POTUS. It was a contentious issue and a means to get the southern states to sign on.

Yes. That's the point. The union was formed based on an agreement that there would be a structural guarantee that low-population states would have outsized representation in the Senate and in selecting the President, as an inducement for them to give up the sovereign prerogatives that would come from being independent of the union. Same as with the EU. Countries gave up some of their sovereignty, with the expectation that the EU government would not be purely proportional to population.

It sure as hell is not the way we should be electing the POTUS now.

Not a given. While we've eroded the sovereignty of States (as States) over time (notably the 16th and 17th Amendments), they still have a unique and important role in our government that's different than almost any other nation on earth. Almost everywhere in the world, smaller administrative regions are the creation of the national sovereign and have no independent sovereign authority. We're almost the opposite here - there are vast areas of government where the States and only the States have power to operate, and the national government is the creation of the States - not the other way around. In that way, we're still very much like the EU government. France and Germany and Italy and Spain and all the other countries created the EU; the EU did not create those countries. Which is why the EU continues to have disproportionate representation, to respect and prioritize the sovereignty of the smaller government members.

It's a compromise, and one that still has important effects that line up with the original "bargain" where low-population states gave up their full sovereignty.