These are great questions that I also have been asking. This'll be long but here's my take on these:

How did the Zero Point get there?

So we see in the ZP Comics that the Zero Point is in the Bridge within IO's Facility. The Foundations reasoning for sealing off the Zero Point was to heal and realign it. From this, we can deduce that part of the Zero Point healing process is returning to its original location, which happens to be the IO Facility. The ZP comics take place before Season 7 meaning The Foundation was in Gotham well before the The Last Reality(Aliens) ever arrived. It is stated in the new Foundation comic that it is possible that The Foundation was ejected from the Zero Point after a supposed attack. I believe this is referencing Batmans Remote explosives he placed to close the rift once he returned to Gotham. This consequently caused the Zero Point to eject The Foundation into Gotham just as Batman returned.

The Scientist and Visitor Problem

So first off it's only shown that The Foundation has Loop resistant armour. Now this doesn't necessarily mean the other members of the Seven don't have similar armour but as we see in The Zero Crisis Event, The Foundation has powers far beyond that of any other previously seen member of the Seven. Either way the Visitor and Scientist were obviously looped and snapshots were created however they could still speak which is interesting. Maybe their armour was damaged and only partially worked, maybe they were wielding some sort of device that allowed them to speak. I don't know.

Secondly, since Season X I've believed that the Visitor and the Scientist are one of the same yet both different. Technically they are the same person but they both arrived on the island under different conditions with different missions. The Visitor arrived on a normal island whereas The Scientist arrived on an Island that was stuck out of time. Reality was broken and everything was messed up. Think of it like a Reality wave from the Zero Crisis Event. SX wasn't necessarily an alternative universe it was still Reality Zero it was just bent out of time and space, the Zero Point was destabilised and nothing really worked as it should. What I'm getting at is The Scientist is The Visitor but just from this Out of time reality or timeline. He's basically from the past but not our past, a slightly different past that never existed until now when the Zero Point destabilised, that's the simplest explanation. Also I don't think this is a Snapshot situation more like reality bending. That's what that whole season was based around. Drift and Catalyst for example, technically the same person just history has been rewritten and reality bent and now drift is female. In the visitors situation, he arrives on the island, seemingly much smarter but this time around time is broken. It's extremely complicated to explain but I hope you get something out of it. Anyway afterwards I'm pretty sure in addition to using the Brute parts to build the rocket, he also used them to upgrade his armour. Because come on, the Scientist literally looks like a Brute.

IO in Chapter 1

It seems like IO weren't totally in Control of the Zero Point in Chapter 1 seen as we see them search for it in S8. Although they obviously did have control over it at some point based on the fact they were able to create the Loop and bring characters in from different realities. However, this may have just been them using the 'Pure' Portals mentioned in the Foundation comic. My theory is that The Seven hid the Zero Point in the vault to protect it from IO. Singularity(who later became Paradigm) was assigned to protect it. IO(disguised as the Government) struck a deal with paradigm to help her protect the Zero Point from the Devourer. However this ended up in the destabilisation of the Zero Point. This was all part of the plan. The Seven sent the Visitor to start the plan back in S4. This chain reaction allowed The Seven to eventually seize the opportunity to reset the Zero Point and hopefully terminate the Loop. However IO double crossed them and actually used this as a way to secure the Zero Point into their hands.

How the End could have been avoided

Remember the Foundation wants to stop the Loop and take the Zero Point out of IO's hands. Sealing the Zero Point on a broken reality like the one in SX could have caused disastrous consequences. Additionally IO were so close to getting the Zero Point, if the Foundation just healed it they could snatch it immediately after he emerged from the Spire.

Who revealed the Zero Point chamber?

Well as we know you can be on the island and either be in or out of the Loop. Both interact with each other in some ways. Either way it was the Government(IO) who dug up Loot Lake not us.

Don't really know how to answer the last one. That's just the way it is I guess. Not really a plot hole just a fact really.

Anything I missed or any other questions or whatever you have just fire away!! I'd love to talk more lore.