unity-js-scopes-tool contains some clever code to attempt to build an npm package with an appropriate cross-compiler if that package contains compilable stuff; this ensures that doing "unity-js-scopes-tool path/to/node_modules somepkg" will build somepkg for armhf so it works on the phone, rather than building it for the host architecture. However, it doesn't work with node-pre-gyp packages; a good example here is sqlite3 (https://www.npmjs.com/package/sqlite3, and https://github.com/mapbox/node-sqlite3). Installing this with unity-js-scopes-tool should first look for a downloadable pre-compiled version for armhf, and then if one is not found (which it isn't because mapbox don't provide one) do a build. However, nothing is built at all, which obviously causes the scope importing sqlite3 to fail at runtime.
To replicate:
1. unity-js-scopes-tool path/to/node_modules sqlite3
2. Observe that nothing is compiled.