I pretty much stick to the diagram below on these matters.
As for the OP. Gibson and Epiphone pretty much make the same guitars, but at different price points. Epiphone generally aspire to use the exact same construction specs (body wood, scale length, neck joint etc) as Gibson, but are doing it with cheaper materials, cheaper staff and possibly less time. The difference in the quality of all this can vary wildly, but for sure an off the shelf Gibson does sound and play a bit, and in some cases, a lot better than an Epiphone. But that doesn't necessarily mean the Gibson represents good value for money.
Comparing Japanese/American Jacksons is a different matter. As far as I am aware, the bulk of Jacksons production line is in Japan and the high end stuff is made in USA. In that case the aspiration of the company itself, is that the better models be made at home, not abroad. Gibson/Epiphone, may be owned by the same group, but they are independent, and to an extent rivals at different price points, and they each have their own distinction between a mass produced standard model and a higher quality model. In simple terms Gibson build both the SG standard and 61'VOS in the US, while Jackson produce the RR5 in large quantities in Japan, while the more exclusive RR1 is US.
In the broader terms of this debate, there is no doubting that Gibson and Fender etc. build good guitars, my main agro is that they are simply overpriced regardless. Looking at the high end; a Custom shop V.O.S 1960 Les Paul costs £4400. I mean fucking hell, are they serious. And ultimately the wood is what the factory has ordered, the cream no doubt, but it's still picked from a bulk order, and they are all built to the same spec, what if the neck isn't quite what you want?
I know a guy who makes
very nice guitars for £3000, he picks the wood from the supplier himself and hand builds the thing over 9 months, he shapes the neck how the customer wants it, and has the pickups custom wound to match the quality of the wood. etc. etc. Whats better in this case? Considering the Gibson comes of a production line (granted a more exclusive one) and the other is custom made, where are the profit margins?

(smug tosser wink sorry!)
The standard priced models suffer the same fate. While I'm dubious of modern Gibsons, Fender are pretty impressive. I went looking for a fender but I came home with a Korean guitar that was half the price. The thing is, some companies take pride in their Asian manufacturing. JHS have wood imported from Canada and north America to make their cheaper Vintage Advanced series. And trust me they sound fantastic. Fret King use the exact same wood and hardware in both their UK and Korean factories. The Korean factory is described as a 'workshop environment', they basically admit all you pay for with a UK build is more time put into the instrument.
Rob