treelike.js

const data = {
  args: [
    ['foo.bar.baz', 1],
    ['foo.bar.biz', 2],
    ['fin', 3]
  ],
  env: {
    'APEX_FIN_BIN': 7,
    'APEX_FAN_BAN': 8,
    'NOPE_NOPE_NOPE': 9,
    'NPPE': 10
  }
};

function setKeyAt(target, keys, value) {
  const tail = keys.pop();
  const leaf = keys.reduce((step, next) => {
    if (!step[next]) {
      step[next] = {};
    }
    return step[next];
  }, target);
  leaf[tail] = value;
}

function resolvePath(path, {del, prefix, clutter}) {
  const rest = path.split(del);
  const [head] = rest;
  if (prefix && head !== prefix) {
    return [clutter, ...rest];
  } else {
    return rest;
  }
}

function treeLike(flat, {del = '.', prefix, clutter}) {
  const out = {};
  Object.keys(flat).forEach(key => {
    const value = flat[key];
    setKeyAt(out, resolvePath(key, {del, prefix, clutter}), value);
  });
  return out;
}

function fromEnv(env) {
  return treeLike(env, {clutter: 'env', del: '_', prefix: 'APEX'});
}

function fromArgs(args) {
  const flat = args.reduce((p, [k, v]) => (p[k] = v, p), {});
  return treeLike(flat, {clutter: 'args', del: '.', prefix: null});
}

console.log(fromEnv(data.env), fromArgs(data.args));