Looking further, the Optiboot bootloader seems to be distributable, given attribution, could you not just use that?
You can definitely use OptiBoot for commercial work with a ATMega328; a lot of projects have done that. The Arduino team itself actually used to maintain their own bootloader (with the Duemilanove & older boards) and switched to OptiBoot with the Uno.
I don't think you'd be able to use OptiBoot directly as a bootloader on an ATMega32u4. It programs the user memory from the hardware serial UART; at a bare minimum you'd have to patch it to read data from a USB virtual serial port etc. That may be possible, but is outside my area of expertise....
While I was able to successfully get my project to work by loading the UNO bootloader when I used the ftdi module, I have not yet finished laying out my recent rev with a 32u4, so dont know if this would work yet.
For personal projects or non-commercial devices yes you should absolutely be able to do this on your own; you can download the Leonardo bootloader hex file from github and there's plenty of posts in the Microcontrollers section of this forum of people using blank ATMega32U4s for Leonardo clones, exactly as you describe. I just don't believe you can legally sell your own stuff with the Caterina (Leonardo) booatloader and the Arduino team's USB vendor ID & product ID.
The FT230X says that the IO pins are 3v3, but 5V tolerant. Looking at the datasheet, it doesn't say if the TXD/RXD are, only CBUS and DBUS...can you safely interface the RX pin to a 5V uC?
No problems at all so far. I copied the datasheet's "6.2 Self Powered Configuration" and "7.5 LED interface" schematics for the FT230x support components, and the Uno's connection -- 1K resistors on RX & TX between FT230x and ATMega328, reset connected with with a) 100nf cap to the FT230x's CTS, b) 10K pullup, and c) reversed diode to +5v.
I apologize for hijacking this thread and like I said before I'm not 100% certain on this. If anyone knows for sure I'd love to hear it!