Well I tried various side mounting schemes and after a lot of fussing decided that top mounting (like here) is really the way to go with such a small box. The problem is that the PMMA window designed to mount over the VL53L0 ranging sensor has a step to allow flush mounting to the outside case and to allow gluing or sealing along this stepped edge for a more or less hermetic seal.
Machining such a complicated shape onto the side of the box proved impossible. But doing so on the box bottom was relatively easy (see above, thank you Greg Tomasch!). I also redesigned the VL53L0 carrier board using a 2-layer design so I could have it made at OSH Park in 0.8-mm thickness and I reduced the width a bit thinking it would be easier for side mounting. The pcb width is now the same as the PMMA window width. The PTHs are designed to be aligned with those on the main board as I was thinking I could use some sort of board-to-board mezzanine connector with the side mounting but I have fallen back to simply soldering wires. I did test the new window location with the old rig by taping the carrier board over its top to hold it in place (the fit is pretty snug though) and placing the main board in its usual place. The main board and carrier board nearly interfere so switching to the thinner carrier board design is really a must for bottom mounting. Although I could stand the main pcb off with washers or something. I ran the test a few days with the device mounted to the underside of the recycle bin lid and got this: