Use Standard Paths option doesn't seem to make a difference either way.
Checking the Verbose option prints out "tried ~/Documents/Music/Pd/patch.pd and failed" for every patch that attempts to be created from those folders.
I also just noticed a strange case where I tried to create one of my abstractions (detune.pd) in an empty patch with verbose output. It fails to load it from a whole lot of places in ~/Documents/Music/Pd/ and subdirectories, but finally succeeds: "tried ~/.local/lib/pd/extra/detune.pd and succeeded". However, this abstraction uses a bondo from the cyclone library, which I have installed at ~/Documents/Music/Pd/externals. Pd tries to find bondo in ~/.local/lib/pd/extra first, but fails repeatedly. At the bottom of the log, I noticed this: "tried ~/Documents/Music/Pd/externals/cyclone/bondo.pd_linux and succeeded". So apparently it is sometimes finding things in my paths? Or this might be because it's part of an external installed through deken? Yet, other externals I've also installed through deken seem to fail. I'm really at a loss.