I haven’t played a ton of stellaris, but I had the same experience. The first few games I manually made my ship designs, and I basically had to pause the game each time I got new spaceship tech (especially if I was at war). The last game I played I had auto make designs on, and it was so convenient. There was just a tiny issue with the automatic design flip-flopping between projectile and laser weapons for some reason. But it was definitely a better gameplay experience to have the auto-designs.