tl;dr

Webpack should produce the same build whether a module is linked or not.

In depth

Considering the following dependency trees:

project@1.0.0
├── babel-runtime@5.1.9
└── sub-project@1.0.0

sub-project@1.0.0
└── babel-runtime@5.1.9

Notice: NPM does not include babel-runtime under sub-project when npm list is called from project.

Webpack builds something link:

[0] multi main 52 bytes {0} [built]
[1] ./index.js 2.08 kB {0} [built]
[2] ./~/babel-runtime/helpers/interop-require-wildcard.js 148 bytes {0} [built]
[3] ./~/sub-project/index.js 2.46 kB {0} [built]

If we run npm link sub-project we obtain the following tree:

project@1.0.0
├── babel-runtime@5.1.9
└── sub-project@1.0.0 -> /Users/fc/Development/sub-project

Notice: babel-runtime still doesn't appear under sub-project.

But building the project again will duplicate its dependencies:

[0] multi main 52 bytes {0} [built]
[1] ./index.js 2.08 kB {0} [built]
[2] ./~/babel-runtime/helpers/interop-require-wildcard.js 148 bytes {0} [built]
[3] /Users/fc/Development/sub-project/index.js 2.46 kB {0} [built]
[4] /Users/fc/Development/sub-project/~/babel-runtime/helpers/interop-require-wildcard.js 148 bytes {0} [built]

Using resolve.root or changing the resolve scope of loaders do not change anything.

Expectations

It would link to be able the link my in-development modules into my project using npm link without having to tweak the webpack config.

The real problem isn't the build size but the unexpected behaviors raised but duplicated dependencies.