Any plan to offer layers of tiles, potentially with different tilesets and/or rules? (this one is desaturated background tiles, this one is actual platforms, etc...)

This feature isn't currently planned -- In the case where the background layer isn't directly connected to the foreground layer (eg. the parallax backgrounds in cave story or shovel knight) the layer could as easily be a separate project. In cases where the background layer is connected, such that you're augmenting existing tiles, eg, adding grass/snow to a brick tile, you'd now have to concern yourself with keeping details in sync on multiple layers which would break the workflow and with it negate a lot of the advantages Tilekit provides.