I backed the Teensy 3.5/3.6 Kickstarter and just got mine, but no time to really look into the details. I'd like to port the SmartMatrix Library to run on the new Teensys, but I'm not sure when I'll get to that. The SmartMatrix Shield was definitely not designed for the Teensy 3.5/3.6: there's a collision between the longer board and the panel connector.
I skimmed through the new pinout, and at a glance it looks pin compatible with the Teensy 3.2. I haven't compared the DMA engines.
Can't promise anything for now, other than I'll look into this in more detail before I work on another rev of the SmartMatrix Shield, maybe sometime in early 2017.