boot.py or running a custom script to load the bitstream during the Linux boot is the easiest way to do this.
Why do you need to load the Overlay after power up?
If you disable FPGA Manager then it should not be included. Can you check if it is included or not in your image build?
You can find some other posts on this.
https://discuss.pynq.io/t/for-v2-5-is-there-a-way-to-have-it-load-a-bitstream-during-power-up-like-it-did-in-prior-versions-of-pynq/572/7
You should check any code that you add to boot.py in a notebook first to make sure it works before adding to boot.py.
Cathal