I thought that the bootloader of 32U4 was developed using LUFA. What about user code? I've been working on the HID core code for a while and just compared what I saw in Arduino IDE 1.6.5-r5 (without PluggableUSB) with LUFA. They were not the same. I also searched a couple of keywords in LUFA's HID driver in Arduino IDE 1.8.5, no hits. So can I say that apart from 32U4 bootloader, Arduino AVR USB development was not related to LUFA?
I wish I could borrow a device class from LUFA and still maintain the arduino stuff in case I need them, such as nice libraries for lots of peripherals. Going with LUFA will be going away from those libraries.