The filter template can be applied to bound columns only, to enable the developer to provide a custom UI for entering a filter value that will be used to filter the data the Grid is bound to by the respective field the discussed column is bound to.
That said, providing an opportunity to use custom template for the filter row cell of the columns that are not bound, seems like a feasible candidate for a feature request. Please submit the idea to our UserVoice portal:
... so we can track it, and consider it for a future enhancement of the Grid package, if it gains enough popularity. Thank you in advance.
Meanwhile, you can access and manipulate the filter row cell of the Command column programmatically, to achieve the desired functionality, e.g.:
I hope this helps.