I thought part of the point of the strange election process we have was to "ensure" that southern states would have a vote even in the face of a more populous north…
They did. Which was why they were able to hold out until 1860 when the writing was on the wall. Since slavery didn't die on it's own and was the underpinning of the economy of many states violence was somewhat bound to happen.
You can't just expect to make any sizeable minority of your nation's economy non-viable and not have all the people's lives you just ruined start shooting. You might be able to get away with it if the people losing out are an evenly distributed minority but if there's a huge block where they are the overwhelming local majority it's gonna get ugly.
The alternative path out of slavery would have been to boil the frog but with the uneven geographic distribution of slavery that wouldn't have been reasonably possible to do socially (e.g. convince people to spend more any more money treating slaves better until wage labor is competitive and slavery can be legislated away without a war). You might be able to boil the frog legislatively but the weak government structures of the 19th century were not well equipped for that kind of thing and that requires a lot of support anyway. In order to get the nation bootstrapped the founders intentionally put off any action for several decades. Something calamitous was kind of bound to happen. Frankly I think we were kind of lucky we got off with a "one and done" war over it (yes I know there was a bunch of background violence after the fact) rather than a perpetual slow boil conflict that turns into a low intensity shooting war every few decades like you see in other parts of the world.
In fact, it was the slave owning southern states that wanted the Senate to be apportioned proportionally, rather than equally (this was the Virginia Plan). The Virginia Plan created a two-chamber legislature with proportional representation based on population. The New Jersey Plan would have allocated one member of Congress to each state. The Connecticut Compromise that led to the current allocation received buy-in from both slave and non-slave states, because it was about small vs large states, which were present in both sides.
The population advantage of the South was the impetus behind the infamous "three fifths compromise". The 3/5 compromise was designed to reduce the interest of slave-holding states in Congress as well as the elections.
The South had more people, but far fewer voters (partially because of slavery, partially because they had more restrictive rules even for white males).
The Senate was done for small states, but the Electoral College was definitely invented to appease the South.
> but the Electoral College was definitely invented to appease the South
No it wasn’t. Under both the Northern proposed New Jersey Plan as well as the Southern proposed Virginia Plan, the President would have actually been elected by Congress. There were concerns that having Congress elect the President would jeopardize separation of powers. So the Electoral College was created, with one elector for each member of Congress. It had nothing to do with protecting the interests of slave-holding states, but instead was designed to make the Presidency more independent of Congress. The fact that the President would be elected by States as opposed to people directly was uncontroversial. What was controversial was whether the apportionment of those votes should be proportional to the population (where both chambers of Congress had proportional votes) or whether it should be the degressive proportionality that we have today (where the upper house has equal representation). The slave-states wanted the former, not the latter, owing to their population advantage.
It’s what’s used to allocate seats in the European Parliament, who vote to elect the President of the European Commission, who is the Head of Government of the EU. In many ways, the structure of the EU is identical to that of the US, especially prior to the passage of the 17th Amendment.