The Atlassian Companion app has an option to "Launch on startup", which creates a registry entry in Windows, for just that.
There is an issue with Windows however, where sometimes, it's unable to launch a program if there's space in between a user name.

For example,
Does not work: C:\Users\user name\AppData\Local\atlassian-desktop-companion\Atlassian Companion.exe --was-opened-at-login
Works: C:\Users\username\AppData\Local\atlassian-desktop-companion\Atlassian Companion.exe --was-opened-at-login

This seems to be a Windows issue, since it should be able to launch the app, even if the path has spaces in it, but it just does not work on certain Windows install for some reason.
https://answers.microsoft.com/en-us/windows/forum/all/on-startup-windows-tries-to-open-a-file-but-cant/420aae7f-be93-4f6b-9bc5-b75d01c0fca0
https://stackoverflow.com/questions/2919286/getting-the-username-from-the-hkey-users-values
https://superuser.com/questions/479105/how-can-i-format-this-path-to-work-as-registry-key-value
https://answers.microsoft.com/en-us/windows/forum/windows_10-other_settings/windows-10-upgrade-issue-with-space-in-username/3ea1a411-2c59-4d2a-bda1-d48b9793231f

Workaround:
We can workaround the issue by editing the registry entry, and add quotes around the whole path.
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run\com.squirrel.atlassian-desktop-companion.AtlassianCompanion"C:\Users\user name\AppData\Local\atlassian-desktop-companion\Atlassian Companion.exe --was-opened-at-login".

This works, but once the App starts, it updates the path again, and removed the quotes, and so we have to do this again before restart, after the app starts.

Suggestion:
We should add quotes around the path as a preventative measure, so that users with this issue are able to have the app launch on startup.