After a quick test it appears the conversion from 1 meter to 1 three.js unit doesn’t work with Blender but it’s also possible the Blender FBX exporter just doesn’t include the units because there’s no difference between setting the units as “none” or “meters” either way the matrix for the default cube looks like this:
[100, 0, -0, 0, -0, -0.000016292067961387602, -99.99999999999868, 0, 0, 99.99999999999868, -0.000016292067961387602, 0, 0, 0, 0, 1]
Setting the scale to 0.01 in the exporter should suffice for now, thanks so much for your help!