I used tilemolester and had custom planar order (2bit and 3bit). But this was years ago. It could be some of the tiles/sprites are compressed. I could have sworn that sprites were stored in 8xN instead of 16xN format, and converted on the fly. But it's been a long time since I looked at it.
Edit: For tilemolester, just edit the XML file to create new planar layouts/formats. I did like 3bit and 4bit sequential, and 2bit interleaved planar + 1bit planar, etc.