For Perforce (and potentially Subversion), it seems that the .uproject file is not added to source control when setting up source control for the first time. Additionally, it seems that any starting content (game configs, game content, and source files for a C++ project) are not added either until they are either modified or loaded. We should also consider ensuring that all content is also added to the initial source control commit, rather than just the content and settings that have been modified.
When using Git, this is all added when the Git repository is first initialized.
1. Create a new project
2. Connect to Source Control
3. Save All Content
4. Attempt to submit to source control
Expected Result: The .uproject file should be marked for add
Observed Result: No files are marked for add.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-36041 in the post.