the recommendation in the pin diagram refers to not using 5V with Bela's own digital pins. So if you are connecting it to external electronics which is happy to receive 5V, then you can use it (actually you should use the better 5V available at P9.07). The important thing, again, is that the 5V never reaches the Bela digital pins. From the MTCH101 datasheet:
The MTO pin can be considered as an open drain output. A pull-up resistor (usually 3.3k~10 k) is needed to interface with a host. The pull-up voltage can be any voltage lower than VDD. This allows a simple interface with a lower VDD host device.
This is ideal for your application because it means you can use 5V to power the MTCH101, its logic and its MTSA pin. You could then have 5V everywhere except for the pull up resistor connected to MTO, which should go to 3v3. Clearly, you are expected to test this first before connecting MTO to Bela, and verify that the voltage at the pin never reaches 5V.