As of Houdini 17.0.360, and 16.5.614, support for environment mapping for asset paths outside the project (Assets/) folder has been added.
A list of key-value pairs can be set in unity_houdini.env starting with HEU_ENVPATH_ prefix. (e.g. HEU_ENVPATH_PROJECT=C:\project\hdas)
These are then checked on every asset file load and the stored path for asset file is remapped to the key part of the pair. (e.g. assetPath=$HEU_ENVPATH_PROJECT\tree.hda)
The environment mapped paths are displayed in Plugin Settings. The path to unity_houdini.env file is now set relative to Assets/ folder.
More information in the docs here: https://www.sidefx.com/docs/unity/_environment.html [www.sidefx.com]