Most products supported as Software Distribution are per request by customers. FileZilla has not been added yet. You use this site to create a quick request for the Content Team, just use Data Coverage under the Enhancement Category drop-down. Turnaround can be surprisingly quick.
Your correct about Custom Patches designed to patch products and not install them, though it can be done. You would need to figure out the switches used to install FileZilla silently and without user intervention. This page will show you where the switches would be added to the custom patch. The detection portion of the customer patch can be as simple as looking for a registry key that would be common in all Filzilla installs. See the Registry Key Tab section.