fix: over extracting native modules with pnpm

[segevfiner]

pnpm results in bundling paths like /snapshot/node_modules/.pnpm/foobar@0.1.0/node_modules/foobar/build/Release/foobar.node

So use the last node_modules instead of the first to figure out what to extract so as to not extract the entire .pnpm folder.

Contributed on behalf of Swimm