In RPG Maker 2003 you can access only two layers for the tiles (below the hero and above the hero). But if you use the picture feature of RPG Maker 2003, you’ll notice, that there are a lot more layers (e. g. the parallax layer, a layer above and below weather effects and so on). However, you only can use them by placing or moving a picture, but not with the normal tiles.
It would be fantastic, if the RPG Playground’s designer would give us both – an autolayering for the most design tasks, but also full manual control, wherever we need this. For this I guess we need some kind of tag to deactivate autolayering for just some tiles. I also had a look at the designers of the newer Makers. If you really implement full layer access, RPG Playground’s designer (regarding layers) would be more powerful than the Makers.
Btw.: The RPG Playground’s designer is already more powerful than the makers, because of its autolayer feature. I pretty much like the autolayer feature. Only in a few cases we have issues like the one I explained here.