IMO, the "a thinnest location, when actually the bore is a 'global' phenomenon" paradox was not present from the before the actual drilling took place. I rather think this derives from Shai'tan on purpose choosing a "focal point" to mass the True Power he could leak globally, and build up his touch on the Pattern from this place rather than applying it globally. Let's say just for example that 80% of the energy he can pass through the barrier is massed and used around SG, and 20% is used to affect other places/the weather etc. and for Moridin and SH's use. It would make sense that Shai'tan chose for the physical manifestation of the "Pit of Doom" a location far away from the likely massive amount of the One Power used to thin out the Pattern (he wasn't looking for a confrontation right away), and far away from the high density zones. where his build up of power would be observed and noticed much sooner. I don't think Shayol Ghul was created instantly by the drilling either - I think it resulted from a slow build up of Shai'tan's power and a gradual alteration of reality there. I think it's probable it took many years before the corruption that started to spread on that resort island was even connected to the Collam Daan experiment. My feeling is in the first years when the corruption was noticed, that weird geologic phenomenons were occuring and that the OP seemed incapable of regulating the weather there anymore etc. the scientists had only theories about what might be causing this stuff. My guess is that it's only after he corrupted the whole area and humans had deserted it that Shai'tan opened a path to the "Pit of Doom". Elan Morin was fascinated by the nature of reality, so I would imagine witnessing the shifts in reality on that island is what attracted him there in the first place, and why it's someone like him who was the first (or one of the first) to eventually have contact with Shai'tan.

As for the incident with the drilling occuring at the location of the Collam Daan, it would seem to me that in the first place the scientists sensed a new source of Power "beyond the pattern", not at any actual geographical point in the world (that would be odd for them to even reason in geographical terms for a source of power, that'd be like trying to pinpoint a geographical location for the True Source, which is everywhere and nowhere). IMHO, the "drilling of the Bore" was thought more in terms of attempting to thin out an outer layer of the pattern so that what was blocking access to this other source of power would become accessible. It may have been a bit like being shielded. My guess is that the first sensing of this other source of power beyond the Pattern probably didn't happen in the "real world" at a location, but more likely in TAR, an IF world or in a vacuole.

As for the destruction of the Collam Daan, it may not be so surprising after the revelations in TGS. It probably occurred when the drilling thinned the layer/shield and the One Power touched the True Power, and the location of that clash was the CD. That happened at the CD pretty much for the same reason the tainting of saidin occured at SG: it's where the TP and OP came in contact within Creation.

That being said, I don't think there's a fully rational explanation for the location of SG vs. the Bore being global and having been drilled at another location altogether etc. RJ created this to remain weird and paradoxical, and the result of a force of chaos, of a universe with one set of rules and a being outside that reality and with other rules clashing with it. Some rules Shai'tan manages to break (eg: altering the nature of reality and the natural laws around SG) but others he is bound by when he tries to act within creation. For instance I doubt space and time exist at all in his prison, but within Creation if he chose to mass his power in one place, then his power base is bound by space. Similarly, in his interactions with Creation and what's within, like souls, Shai'tan is bound by Time).

I think with the Bore RJ was aiming for something our science can't explain anymore than the AOL scientists could. Even the Forsaken seem to look at the Bore paradox from the "*shrugs*/it's just how it is" perspective. For the Bore, I wouldn't be surprised RJ used his knowledge of science not to come up with something logical bit to create something that would defy explanation.