Sorry that you encounter such problem. We are currently working on the issue. Please vote for the issue https://youtrack.jetbrains.com/issue/TBX-1817 to follow the progress.

We’ve updated the JetBrains Toolbox browser extension, it can now clone and open files from private instances of GitHub, GitLab and Bitbucket in JetBrains IDEs. Please check it out now.

Currently it's not possible to change the default applications, but we are working on the issue. Please vote for it at https://youtrack.jetbrains.com/issue/TBX-1817 to get the news on its progress.