Yes; our FoxTrot hidden preferences page has been updated:
The name of the folder containing a file is normally indexed as part of the “other metadata”, allowing to find files directly in this folder by searching the folder name. If you want to index the relative path instead (full path of the file, stripped from the path of the indexed folder), so you can find all files at any depth inside a folder (this requires rebuilding the index):
defaults write com.ctmdev.FoxTrotShared UseRelativePathForParentFolder -bool YES