You don’t have to change the folders regularly. Just once if they’re not showing up in the results at all.
Like I said, Alfred primarily sorts by its “knowledge”, which is its memory of which item you selected for which query.
Modifying the folder is just a way to get an item into the results list in the first place so you can “train” Alfred.
Alfred is tuned for performance, while Finder and Spotlight are tuned for comprehensiveness.
You get much better results from Alfred by keeping searches focussed. So if you want to find folders, you configure your File Filter to only search for folders instead of any type of file.
It’s fairly straightforward to set up a two-step search that first filters folders and then the files within the folder you selected. I believe one of the built-in example workflows demonstrates this technique.
