Multiple git profiles especialy with Atom I have configured Git to use a specific CA certificate, but how can opt-out for it other than using the switch -c http.sslVerify=false? (or enforce other certificate which seems better in terms of security).

Okay, a workaround was to create a shell script for a shortcut and use it like

gitf clone


That is okay for a quick test in a secured and trusted environment but it is a potential security breach. Do not try this at home.

The real gotcha comes then in if I would like to use the Atom editor. Somehow I cannot find an option for the git executable.
You'd better add this CA to a bundle of valid CA and keep using it for all cases with 

git config --add --global http.sslcainfo=/path/to/cabundle
git config --add --global http.sslbackend=openssl


Using https://curl.haxx.se/docs/caextract.html as starting CA bundle sounds a good idea in my opinion.