They may have changed that behavior recently. I was trying out pipenv last week and running `pipenv run script.py` in a subdirectory printed a message along the lines of "Courtesy notice: no pipfile found in this directory. Using pipfile in [project_root]. Behavior can be customized by specifying a pipfile with [some_flag]". I'm fairly sure, but not positive, that I also was able to install modules from subdirectories into the project venv like you want.

On mobile; I may be misremembering some details. Would encourage you to check new version behavior if you're interested.