OS X El Capitan & Android Studio 1.4
After further work on this, I found something that seems to work. I RTM'ed the man page of launchctl, and noticed the config-subcommand. So this is what I did:

sudo launchctl config user path "paths:I:want:GUI:apps:to:use"


Then reboot, as launchctl instructed me to do.

I had added a debug print statement to my gradle file:

println System.getenv("PATH")


After rebooting, build printed out the changed PATH including those parts that I added via config user path.