It would be great to give Inventor Bolted Connections an extra tick box called "As Custom", for when the bolt that the user is inserting is unique, requiring to be saved to the workspace for further modification (such as a being drilled).
Custom bolts, washers & nuts would be displayed under the File Naming list, where they could be assigned a custom name before being saved into the users workspace.
The current workaround for this workflow is to manually create a custom bolt, then run the "Replace" command on the standard bolt to replace it with the custom bolt.