Is there a way to modify the timeout? I do not want to compromise on the coverage of the version update check.
For version update configuration, GitHub official documentation states the ways to cater for the timeout but these means are controlling the depth and coverage of version update scan.
update-types: ["version-update:semver-patch"]
For the timeout, its root cause is mentioned in: https://docs.github.com/en/code-security/dependabot/working-with-dependabot/troubleshooting-dependabot-errors
Dependabot timed out during its update
Dependabot took longer than the maximum time allowed to assess the update required and prepare a pull request. This error is usually seen only for large repositories with many manifest files, for example, npm or yarn monorepo projects with hundreds of package.json files. Updates to the Composer ecosystem also take longer to assess and may time out.