I don’t think that you can do what you want to do - I don’t think that closed checks are still mature. There are many outstanding promotion requests for private registrations. It might be worth adding this as a request. Even hidden folders are at the folder level, not at the file level.
From MSDN:
Automatically Launching Gated Check-in Builds
A gated registration assembly is performed automatically when any of the following events occur:
The row was defined using the Gated Check-in flag selected on the Trigger tab of the assembly definition.
Someone is trying to check one or more changes that intersect with any of the displayed folders in the Workspace tab of the assembly definition.
Even if you add the tag *** NO_CI *** and try checking, it will run the check to create changes.
The obvious workaround is, of course, checking the checkbox ignoring the need to create an assembly (the path I'm sure you're trying to avoid).
If we look at the user interface around editing the assembly definition, there are no optional parameters for the rules, etc. All that matters is the mapped folders.
However, you can set specific folders that will not be created by masking the workspace folder. However, if you do, it will not collect these files for assembly at all. So if you had all your JS files in one folder and excluded them from the assembly using hidden approaches, the assemblies would not work if you really want to start the assembly.