As an update: I've spoken to Ronnie who guided me on how to access the stern thruster. It's basically under the swing bench. Here's how:
1. Remove bottom cushion on swing bench, removing three screws
2. Remove the two larger bolts holding bench to boat. One is accessible on both sides, but the other requires you to remove the cupholder to access.
3. Remove 4 screws holding lid (the flat top under the swing bench)
4. Remove 4 screws holding tub, remove tub.
5. Remove 4 screws from front small panel in front of tub (this will allow better reach when removing thruster)
Stern Thruster should be visible on bottom right. The exhaust hose is in the way but can be moved or removed for better access. There's another scupper hose which can also be removed (I noticed mine actually had a slit/leak, so I replaced).
Now for the fun, removing the two bolts holding the thruster. I was able to get one off with 6mm hex wrench, but could not remove the right one, due to torque. I understand there's a special tool, which Ronnie is sending, so not fixed yet. We'll see and report back, but definitely harder than changing the bow thruster.