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When are you new to QGIS and PyQGIS what works in the background you might be confused by the different Python Interpreters and customization by settings so called environment variables. How do avoid such conflicts?

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You do this by adding specific environment variables or starting QGIS out of script what sets custom variables as it is done when you doing PyQGIS development.

The environment variables aren't set by any installation process although the description allows such interpretation. If you want that QGIS uses different/additional startup scripts or plugins you have to create the corresponding environment variables by yourself. This process is well descriped on How-To Geek.
You can add custom variables in QGIS itself via System Settings what even can override system's environment variables.

If you don't want to mess up with your standard (production) profile you may want to create an extra profile folder and [change the path default from default profile folder “.qgis2” to the new one].(How to change default path for ".qgis2" folder on Windows?)

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