You haven’t said which device you are using - for Raspberry Pi devices you can set device tree overlays and parameters via the Fleet Variables or Device Configuration sections of the balenaCloud dashboard. Details on this feature are available here - Advanced boot settings - Balena Documentation
The device tree that I’m using for my project is not “approved” so that method won’t work because it’s not present in the overlay folder. I think I confused you with the word custom as most of the DT overlays are custom. I’m talking about a devicetree that is not included with balena and it’s not present in the rpi linux kernel dts folder.
I think it might be possible to add your own custom.dtbo to the boot partition (/mnt/boot/overlays in HostOS) and then add the dtoverlay=custom parameter.
I haven’t tried this myself though.