That’s why you use the virutalenv … if you install platformio into a virtualenv, it doesn’t touch the rest of your python install. And yeah, it would the pretty much the same to any Linux install. If you install it via IDE, say VSCode, it would be entirely different… even on linux it uses virtualenv, so it doesn’t touch the rest of your system.
Anyway, that’s beside the point…
I believe the current way to configure values that you would normally configure via menuconfig is to use a sdkconfig.h file in your \src directory - i.e. manual edits. Going by this post and comments on Github, Ivan is mainly waiting on espressif to make changes to their build system, unless that has since happened?