If you use Sketch > Export Compiled Binary in the Arduino IDE to compile the sketch, the .elf file will be saved to the build/<board identifier> subfolder of the sketch, where <board identifier> is the FQBN (fully qualified board name) of the board you are compiling for, with the : separators replaced by .
For example, if I compiled a sketch named "MySketch" for the Arduino Uno board (FQBN is arduino:avr:uno), then the compilation output will be at MySketch/build/arduino.avr.uno.
Another option is to modify the Arduino boards platform that adds support to the IDE for the Aurix-based boards. You can customize how the build process works in the platform.txt configuration file. You might find pre/post build hooks especially useful for this purpose.
In order to facilitate porting your modifications through updates to new versions of the Aurix boards platform, you can place them in the platfom.local.txt configuration file rather than in platform.txt.