By default,

$ gsettings get org.freedesktop.Tracker.Miner.Files index-single-directories 
['$HOME']
$ gsettings get org.freedesktop.Tracker.Miner.Files index-recursive-directories
['&DESKTOP', '&DOCUMENTS', '&DOWNLOAD', '&MUSIC', '&PICTURES', '&VIDEOS']

This has the effect of excluding sub directories of $HOME, and their contents, in the GNOME Shell Activities Overview search.

In my view, $HOME should be removed from index-single-directories and added to index-recursive-directories. I can't find anything suggesting this was intentionally set as is, but I realize that this may have been set for resource reasons. For what it's worth, after changing this setting and re-indexing, I haven't found Tracker to be a resource sink, and I have a lot of crap in my home directory.

This is related to, but distinct from T4500 -- same effect, different cause.