The transponder is ranked #2 on my personal list of things I’ll surely NOT NEED thanks to my habit of rather hitting than avoiding lokal trees and my “seriously non-pro” flying skills (#1 btw is all this “seriously pro / yaw dropping / designed for racing” lingo on the web page).
To me, the board alignment looks o.k. on the photo as the MPU9250 is mounted such that the USB port looks sideways with default orientation in CF.
Nice for building quads would have been to route the motor outs to the corners of the board.