GibFen

It's possible the pup routes were cut wrong and then the pups installed incorrectly. But then that too is a manufacturing problem. The bigger concern for me is the centering of the strings on the fret board. Again, if all the parts are installed correctly, then the string should form a straight line from the tail piece all the way to the nut slot, and the string should be as much over the center of the pole piece as possible. If all those individual parts are off here and there the end result can look awful and at worst have intonation problems and/or not have proper fret board spacing where he low strings may be too close to the fret board edge or the opposite where the high strings are too close to the fret board edge. When that happens playing feel suffers and can make bending on the higher strings feel very odd. In all that's a faulty and badly made guitar that needs to be rejected, and it should have NEVER left Gibson's plant for retail sale, imo.

Yes, the saddle notch should be placed so that the string maintains alignment with the pole pieces. The strings should go over their respective pole piece, and string spacing should also be correct maintaining a straight line from, the saddle to it's nut slot, and that should really start at the tail piece. IF the tail piece and bridge are set properly then the notch should be pretty close to the center, but it won't be exactly there as the bridge is set at a slight angle, but still pretty much in the middle. The problem is that too many tail pieces and/or bridges are not set properly in the first place as the holes were likely not drilled in the correct position. Tail pieces and bridges are exacting pieces by manufacturing process. Placement of the holes improperly is where the problem can happen and start that then results in having strings leaving the tail piece at an angle in order to compensate for improper placement of the TP and/or bridge. The saddle slots are then cut to try and compensate and align the strings route over the pole pieces and then onto the strings nut slot, while maintaining proper string spacing and centering on the fret board. But, in the case of this guitar it's clear that things were not set/built properly as demonstrated by trying to install a new bridge, with properly pre-cut saddle,s at the proper position that resulted in the strings not being in alignment and not centered properly on the neck. The new bridge and it's pre-cut slots assumes the tail piece and bridge are/were properly installed in the first place. I've seen this big flaw on a lot of ES guitars and frankly it's not acceptable though people do accept it. I rejected a good number of ES335's precisely because of this issue. I don't like the strings to hit their saddle slot at a side angle/laterally. It adds an odd stress point that's going to wear the saddle notch oddly over time and could cause intonation problems. I've had a guitar, not a Gibson, where the bridge was not set properly and I had intonation problems with it for years. I finally called the manufacturer, Schecter, and asked for help. They asked for pictures and how I did the intonation. I sent picts and explained. They asked for the guitar to be send to them for evaluation. What I suspected they confirmed. The guitar has a lifetime warranty and once Schecter saw the problem they warranted the guitar and offered me a brand new one, which was just reissued this year. I accepted and they sent me a brand spanking new one and it's fantastic, better than the original I bought in 2005. That's excellent customer service. OP, I suggest contacting Gibson to see if they too will honor their lifetime warranty and correct the improper placement of either the tail piece or bridge like Schecter did. I'm really curious to read what Gibson does about it. Please post the results.