Layers are currently not supported, the main issue is there not being an obvious solution to implementing them that would maintain the fast workflow Tilekit tries to provide. If layering were to be implemented, I'd want to avoid doing so in the naive way (eg. having multiple layers, each with their own map data and rulesets) without first putting effort into coming up with a better solution which doesn't involve having to manually keep two separate layers in sync with one another.
One of the core goals of Tilekit is to make tilemap editing fast and less tedious, ideally an approach to layers would keep in line with the current level of automation which is already provided.