IMO layers’ drawing order should be like in GIMP, Photoshop, Paint.net and similar software (first layer in “stack” is drawed last). This will make it easier to convert for people who used said software in the past.
Layer order was changed several months ago to display top layer on the timeline = front layer on the canvas. If that change isn’t reflected in the 0.5.4 release, it should at least be in the last nightly build.