The width of a Line does not make difference when strokeWidth=1 or strokeWidth=2, but if strokeWidth=3, the difference will be very obvious.
Is it a precision problem? Below codes can be used to reproduce and the screenshot is attached

import javafx.stage.Stage;
import javafx.scene.Scene;
import javafx.scene.text.Text;
import javafx.scene.text.Font;
import javafx.scene.paint.*;
import javafx.scene.shape.*;

Stage {
    title: "Application title"
    scene: Scene {
        width: 250
        height: 100
        content: [
            Line {
                startX: 0, startY: 49
                endX: 200, endY: 49
                strokeWidth: 1
                stroke: Color.BLACK
            }
            Line {
                startX: 0, startY: 59
                endX: 200, endY: 59
                strokeWidth: 2
                stroke: Color.BLACK
            }
            Line {
                startX: 0, startY: 69
                endX: 200, endY: 69
                strokeWidth: 3
                stroke: Color.BLACK
            }
        ]
    }
}