The way it's implemented now (top to bottom) goes against all the standards regarding layers system, and it's extremely counter-intuitive, also makes things more difficult for people coming from other 2D packages.
Layers and modifiers are completely two different things, so I think consistency doesn't apply here.
Basically every software out there works like this:
Modifiers: Top to bottom
Layers: Bottom to top
I think it would be wise to follow those standards.
And let's not forget that layers systems are a very visual thing, so they need to look right. ?
Cheers.