Preserve Modules Directory Structure Issue/Feature Request

This reproduces an issue with rollup while using @rollup/plugin-node-resolve and @rollup/plugin-commonjs in combination with the preserveModules output configuration.

System Dependencies

Tested on Linux Mint 20 with these node/npm versions:

$ npm --version
6.14.8

$ node --version
v14.9.0

Installation

• Run npm ci.

Reproduction

• Run npm run build
  • Inspect the dist/ directory and notice that the input module is output to dist/src/index.js
• Run npm run build-no-plugins
  • Inspect the dist/ directory and notice that the input module is output to dist/index.js

Ideally, there should be a way to ensure that the input of src/index.js always goes to dist/index.js.

This boils down to differing preserveModulesRelativeDir values changed while using @rollup/plugin-node-resolve.