Then the temp obstacles will be rasterized onto those 2D areas and build into pieces of navmesh. The idea is to try to limit the changes of a temporary obstacle processing to as local area as possible and to speed up the generation process in general by making the input data simpler.
Each layer stores area type and 2D heighfield. The area types should compress really well with RLE, and it should be possible to compress the heighfield using a simple linear spline fitting. Add LZ compression on top of that and the aux data for generating new tiles should not be a huge burden anymore.
Interestingly, this layered heighfield data is also something that can be used to make 2.5D HPA* (the papers so far have used 2D data). If someone out there is up for the challenge, let me know and I'll help you to decipher the data Recast creates.