The mosfet is better. It especially helps for USB host on Teensy 4.1. Of course USB host still works on Teensy 3.6, but often the connected USB device (or hub) gets about only about 4.4 volts.
Back in 2012, when Teensy 3.0 was designed, I wanted to use a mosfet, but none I could find any with low enough on resistance which fit the PCB space and budget. Or at least not at normal distributors where PJRC could buy them. Later Teensy 3.x reused the same diode chosen in 2012
Later in 2018 when Teensy 4.0 was designed, many more parts were readily available. Small size P-channel mosfets rated for high current were fairly easy to find and distributors actually had stock (oh those easy days before the pandemic). So I was finally able to drop diode and go with a very low on resistance mosfet.