You must reflash the chip with the new imu rotation or use automounting.

My case for my SlimeVR full body trackers broke so I decided to make my own version that also shrinks it down a little bit. Install the pcb into the lid first, it's best to try are route the extra bit of the battery cable up in that section as well. It's meant to be a snug fit and I did a bunch of versions on my A1 but you may need to tweak the tolerances for your machine. It's also why I provided the STP file. Leave the original foam pad on the battery, snap the 2 halves together and you're good to go!