Use FlxCollision.pixelPerfectCheck() to check if any of pixels of a FlxSprite overlaps the pixels of another FlxSprite.

FlxCollision.pixelPerfectCheck() will return true if it detects an overlap, and false. if it does not. this is true regardless of the sprite’s hitbox, and works for any scale, angle or even scrollFactor

// overlaps will be true if the two objects are overlapping each other
overlaps = FlxCollision.pixelPerfectCheck(spriteA, spriteB);

Demonstration

package;

import flixel.FlxG;
import flixel.FlxSprite;
import flixel.FlxState;
import flixel.tweens.FlxEase;
import flixel.tweens.FlxTween;
import flixel.util.FlxCollision;

class PlayState extends FlxState
{
	var circle:FlxSprite;
	var box:FlxSprite;
	var overlaps:Bool;
	
	override function create()
	{
		super.create();
		
		box = new FlxSprite("assets/bigbox.png");
		box.screenCenter();
		box.angularVelocity = 180;
		// tween scale up and down
		FlxTween.tween(box.scale, {x: 0.5, y: 0.5}, 2 / 3, {type: PINGPONG, ease: FlxEase.sineInOut});
		
		add(box);
		
		circle = new FlxSprite("assets/sprite.png");
		circle.screenCenter();
		// move right so it only touches at certain angles
		circle.x += (box.width + circle.width) * 0.55;
		add(circle);
	}
	
	override function update(elapsed:Float)
	{
		super.update(elapsed);
		
		final overlaps = FlxCollision.pixelPerfectCheck(circle, box);
		box.alpha = overlaps ? 0.5 : 1;
	}
}