When you bake effects, the editor will "Mirror" the PopcornFX project's directory structure into the target baking output folder (here, StreamingAssets/PackFx).
Your PopcornFx project being located at e:/project,
this means that the source_art folder will be considered part of the popcornfx project folder structure, hence being mirrored too.
The way to fix it is either to re-organize your project's pack folder structure, or define the root location of your popcornfx project in:
e:/project/source_art/VFX instead of e:/project
For an effect located at:
this would lead to the following streaming assets folder structure:
Note: If you choose to move your popcornfx project root location, don't forget to modify accordingly the baking platform path.
Hope this helps.