The image below was made to discuss changing lug angles. However, it illustrates how the chainstay/ seat tube angle will change with bottom bracket drop.

This angle will also change when changes are made to the seat angle, or to dimension E in the chainstay dialog box which shifts the attachment point of the chainstay up and down the back side of the bottom bracket shell. Different rear dropouts will also have different attachment points for the rear end of the chainstay. Different attachment points will result in different chainstay angles and therefore different chainstay/ seat tube angles.