I managed to solve the node_modules issue.
The problem is that meteor puts the node_modules in a folder called “npm”. So, the paths where node looks for the modules are all wrong. Node looks for node_modules folder in the app directory and all its parents but will never look for it in npm/node modules. The solution was just to change the paths like this, I added this on the top of the scripts to alter the paths:
let cache = require('module')._cache;
let paths = cache[Object.keys(cache)[0]].paths
paths.forEach(p=> paths.push(p.replace(/node_modules/g,"npm/node_modules")));