Everytime I start Source Tree, my .gitconfig file is overwritten, which leads to me not being able to access my repositories due to missing proxy server entries in the .gitconfig.

This appears to be a bug, as Brian Ganninger confirmed in reply to my question:

https://community.atlassian.com/t5/Sourcetree-questions/How-can-I-prevent-Sourcetree-from-overwriting-my-gitconfig/qaq-p/757138

Unfortunately, the following thread did not solve the problem, because the setting "Allow SourceTree to modify my global Git and Mercurial config files" is reset to "true" everytime I start Sourcetree.

https://community.atlassian.com/t5/Sourcetree-questions/Why-does-SourceTree-automatically-update-my-gitconfig-file/qaq-p/414282