Quality springs should not "settle" according to Eibach, Swift, and Hypercoil. However, new dampers may have some friction in seals and the damper pistons that may change over time. We noticed that with new KYB struts that took a few hundred miles to "break in" and stabilize. Another issues can be suspension bushings taking a "set". Toyota recommends torquing bushings with the car loaded at normal height, or as they put it "stabilizing the suspension". This should leave the bushings unstressed at normal height. Change the height, and a small amount of twist is added back into the bushings, which may change over time. People who have torqued suspension arms extended with OEM bushings and then loosened and re-torqued with the car loaded have found a difference.
As an aside, Tein S springs on KYBs is a pretty unpleasant combination as the KYB are designed for stock springs and have too much compression damping and too little rebound for the stiffer springs. With restricted travel from lowering, they can be pretty harsh on rough roads, especially with stock front bunp stops as the much lower static height is very close to hitting the bump stops.