I own an sx tele and and agile lp copy, The agiles a 3100 its one of the higher end ones. Its a decent guitar, it plays very well, it sounds really nice with the stock pickups, it has good fretwork and good quality hardware. The higher end stuff is made in korea and probably comes close in quality (i my opiniion) to the ltd deluxe series. I would say the LTD deluxe series has better finish quality ( attention to detail ), and the LTD deluxe hardware is a little better. The agiles are hard to beat for the price. I belive they are all made in Korea. I would say if there is and ESP, LTD Deluxe or Edwards that is close to what you are looking for buy that, If not and their is an Agile that fits your needs better, give it a shot. I don't know anything about the agile custom order but the quality should be similar to what I descibed. As far as I know their customs are not made in a special custom shop, they will be made on the same production line as the regular agiles, just as a special run where they use the parts and woods you specify.
The sx actually played surprisingly well. its the upgrade sx tele ( an extra $25 ) It is a solid ash body, maple neck, with a figured maple fretboard. The hardware on it was absurdly cheap, sadly the hardware is so non standard it would be a major effort to upgrade it. and the frets started showing wear after about 4 years of light to moderate use. Hard to complain for a guitar that cost $125 but I wouldn't buy another one.