Currently this is difficult to achieve using opacity. You might be able to approximate it by creating the same opacity animation on the two layers and then offsetting the animation. But as you say, it’s hard to get the timing right.
Maybe the better approach would be animating the depth positions of the two drawings, by holding the record button while you move one of the drawings before and behind the other one.
You probably still have to find a creative solution so you don’t see the two layers overlapping, such as painting a background area in each layer so they completely cover each other.
All in all - there’s currently no ideal way of creating images sequences. We’re considering creating this feature in the future.