I'm not gonna tolerate much more of this tolerance discussion!
Seriously, it might be possible that Epiphone had to scramble to increase production due to much better than expected demand. Remember the price bump, probably done to trim the demand by a few percent (while not hurting the bottom line). And remember the tuner change up in mid stream, probably also in an effort to meet increased demand that outstripped their original inventory. I wouldn't be at all surprised to find out that some production has been shopped out to other CNC shops in the area in order to meet demand. I've had to do that in the past with my machine shops in China and Korea. What I ended up with was exactly what we're seeing on the newer Eppis - slightly different products close enough to the original design specs to approve but at the limit on acceptability. Different shops have different equipment, different operators, different programmers, different QC processes and different production goals. That stack up in differences could easily result in the minimal body and neck thickness dimensions we are seeing.