vscode-python: pylint extension-pkg-whitelist=cv2 not working only when through the extension (Anaconda)

Environment data

• VS Code version: 1.42.1
• Extension version (available under the Extensions sidebar): 2020.2.64397
• OS and version: Win 10 64 bit Home
• Python version (& distribution if applicable, e.g. Anaconda): 3.7.6 64-bit Anaconda
• Type of virtual environment used (N/A | venv | virtualenv | conda | …): conda
• Relevant/affected Python packages and their versions:

pylint 2.4.4
astroid 2.3.3
Python 3.7.6 (default, Jan  8 2020, 20:23:39) [MSC v.1916 64 bit (AMD64)]

• Relevant/affected Python-related VS Code extensions and their versions: Code Runner 0.9.16
• Jedi or Language Server? (i.e. what is "python.jediEnabled" set to; more info #3977): Jedi
• Value of the python.languageServer setting: Microsoft

Expected behaviour

If I set argument "python.linting.pylintArgs": ["--extension-pkg-whitelist=cv2"], the linter should look up members in the cv2 module.

Actual behaviour

Steps to reproduce:

1. Open a script that imports cv2 in VSCode.

Logs

Output for Python in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Python)

> ~\Anaconda3\envs\cv\python.exe -m pylint --extension-pkg-whitelist=cv2 --msg-template='{line},{column},{category},{symbol}:{msg}' --reports=n --output-format=text s:\shared\new_scripts\cvprocess.py
cwd: s:\shared\new_scripts
##########Linting Output - pylint##########
************* Module cvprocess
...
61,8,convention,invalid-name:Variable name "nh" doesn't conform to snake_case naming style
67,12,error,no-member:Module 'cv2' has no 'imread' member
68,22,error,no-member:Module 'cv2' has no 'threshold' member
68,35,error,no-member:Module 'cv2' has no 'imread' member
68,66,error,no-member:Module 'cv2' has no 'THRESH_BINARY' member
69,18,error,no-member:Module 'cv2' has no 'Canny' member
71,12,error,no-member:Module 'cv2' has no 'HoughLinesP' member
25,27,warning,unused-argument:Unused argument 'time'
...
-------------------------------------------------------------------

Your code has been rated at -5.48/10 (previous run: 2.86/10, -8.33)

Output from Console under the Developer Tools panel (toggle Developer Tools on under Help; turn on source maps to make any tracebacks be useful by running Enable source map support for extension debugging)

(cv) S:\shared\new_scripts>%userprofile%\Anaconda3\envs\cv\python.exe -m pylint --extension-pkg-whitelist=cv2 --msg-template='{line},{column},{category},{symbol}:{msg}' --reports=n --output-format=text s:\shared\new_scripts\cvprocess.py
************* Module cvprocess
...
61,8,convention,invalid-name:Variable name "nh" doesn't conform to snake_case naming style
25,27,warning,unused-argument:Unused argument 'time'
...
-------------------------------------------------------------------
Your code has been rated at 2.86/10 (previous run: -5.48/10, +8.33)

This was originally posted as a pylint issue but they diverted me here. It is really weird that running the same exe (I hope) with the same arguments results in different outputs. My terminal is set to Anaconda Prompt in the workspace.

Similar issues I found: #99, #606, #1648, #1993, #2879, #3562, #3802, #5257