On the CNC machines thing...the guitars aren't apparently made entirely with CNC at all. I have tested a few Epi SG's (when I bought my Prophecy) and there's several differences between the models.
The Epi 'Custom Shop' guitar vs. the Prophecy I went thru with a very keen eye...several spots are a touch different. Even the body shape/size isn't exactly the same but there can be differences by even several millimeters. The neck joint is differently done on them. The pickup cavities aren't even exactly aligned, if you really measure them exactly, they seem to seldom be 100% straight between the two - in fact on my prophecy the neck pup cavity is at least 3mm slanted to the side, with the pickup installed the difference is only like 1mm and you can't see it there but if you measure the gap it widens clearly...noticed it only when making a plexi pickguard for it.

On some Epi's you may find a rather thin lacquer and on some there are spots like the headstock end where there can be like 3 mm thick spots of lacquer to even out a mis-shaped or too small part or something.

I think the Epi's and most other guitars are only roughly CNC'd to rough shape and lots of the shaping/sanding/ cavities etc. are still done by hand & routers.

On the subject of cheaper Epi's...well the cheaper ones obviously have bolt-on necks, and made with inferior woods, usually with thicker necks so that they'll stay straight even if less quality wood.
If you sand off the pain on a cheaper end Epi, you'll likely find dark spots / branch spots and / or color defects in the wood used and deeper dings filled in before painting.

On pretty much every Epi except the very top end ones the woods aren't what they seem. Korina Explos etc...the entire lines are actually veneer coated & made from smaller bits glued together. The veneer is so well done though you literally need a magnifying glass to tell the seams, and it's only easy to find out the deal if you break the surface with a deep ding.

At least on cheap bolt-on epi LP's the top wood isn't even wood but some kind of photo or something.

Having said all that, I really dig many an Epi. I like my Prophecy much better than most any Gibson SG I ever tried, it's a terrific guitar, but still it's acoustic sound will never be anywhere close to that of a Gibson that's made from one piece quality woods and thin lacquers.

Me, I care not about that because to me guitar woods make like 0.0001% difference in the amplified sound anyway.

But trust me, there certainly are LOTS of differences between various Epiphone models and price classes.