I see the same, and even after running the iwd script my logs look like yours.
[Instruments] On xcode 7.0+, instruments-without-delay does not work, skipping instruments-without-delay
[debug] [Instruments] Found Insruments-Without-Delay: /Users/chrigrah/npm/lib/node_modules/appium/node_modules/appium-ios-driver/node_modules/appium-instruments/thirdparty/iwd7
However, until you run the iwd script and see the correct paths in your .plist like I've described you should observe your tests have a forced 1 second delay between every command. At least I did, even when seeing those lines in my Appium logs.
Run the script and successfully add the correct paths to your .plist, you'll STILL see the exact same Appium logging (with the old Appium paths to .iwd) but your tests will run much faster since there's no 1 second forced delay.