Each version of Blender will store the config file in different locations, so running 2.79 and 2.83 together shouldn't be an issue, even if you don't do anything special to set them up. However, if you want different iterations of the same version (like 2.83.3 and 2.83.6 and 2.83.1) then you'll need to add the new config file manually, or they will all share the same configurations, which could screw it up. Same goes for 2.9, 2.9.1, etc.

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