Leviton usb charger into an old handy work box
To start, all devices should be mounted flush into the wall unless they are designed otherwise. This is to prevent fire and shock hazard. Leviton and other devices are giving you a box size not only to fit the device but provide air space for heat disbursement. 

NEC Article 314 has instructions on how many devices by cubic inch, wire splices, and number and size of conductors you can put into one box. I would follow that rather than instructions in a box or someone who would say it it fits it's ok. 

Is there any way you could remove the box and install a cut-in or remodel box that is a required size? If I could that's how I would go.