If you install OpenTracker 5.1b13 or later, Tracker will respect a new setting in ~/config/settings/Tracker/TrackerSettings:

SortFolderNamesFirst on

If your TrackerSettings file doesn’t have this line, add it. If it has it but it’s turned off, turn it on. Restart the Tracker and you’ll find that when Tracker is in list view, all folders are listed before all files, which can help to organize things visually.