QSWAT3_12 is for versions of QGIS 3.34.6 or later that use Python 3.12. This is the default version to choose if you are unsure.
QSWAT3_9 is for versions of QGIS at least 3.16.14 and at most 3.34.5 that use Python 3.9
QSWAT3_64 is for earlier versions of QGIS that use Python 3.7