I'm usually loathe to post to an ancient topic, but since this post is near the top of search results for "adafruit rfm69 bonnet mysensors" I thought this would be the best place to post the solution to the OP's problem.

By doing the following, you should be able to get an Adafruit RFM69 Bonnet on a Raspberry Pi Zero talking to your other RFM69-based MySensors nodes:

1. I started by checking out the head of the development branch (specifically commit aa76d26615, which was the head at the time, but hopefully future versions will work too).
2. I commented out the code that prevented toggling the CS_PIN as @paulsp described in post #1
3. I then built mysgw on my Rasperry Pi (happened to be a Pi Zero, but hopefully that's irrelevant) using the following command:

./configure --my-transport=rfm69 --my-rfm69-frequency=915 --my-is-rfm69hw --my-gateway=ethernet --my-port=5003 --my-rfm69-cs-pin=26 --my-rfm69-irq-pin=15 --extra-cxxflags="-DMY_RFM69_RST_PIN=22" --spi-spidev-device=/dev/spidev0.1 --spi-driver=SPIDEV

With this configuration, I was able to successfully get my RPi-based gateway using an Adafruit RFM69 radio bonnet talking to (and receiving from) various Moteino-based MySensors RFM69 nodes. I think the key difference was that I had to tell the MySensors gateway to use the spidev driver with the --spi-spidev-device=/dev/spidev0.1 --spi-driver=SPIDEV flags (instead of the BCM driver, which is the default).

Obviously if you're using a different frequency for your RFM69 radio (or a different gateway type or port) you should adjust the --my-rfm69-frequency=915 --my-gateway=ethernet --my-port=5003 flags appropriately.