I am working on a project based on Arduino design. Here is the background story that made me consider contacting Arduino LLC. There is a trademark issue related to Arduino USB vendor ID etc. that I would like to raise. I am considering using the ATMEGA32U4 processor that Arduino Leonardo and Micro are using. I also want to use the Arduino bootloader. The bootloader contains Arduino's USB vendor ID and device ID. If I use this bootloader, then my device would identify itself as if it were an Arduino. This is an issue. I am willing to work with you before I put this product into any scale beyond prototyping and testing. I don't have the skills to make changes to bootloader or recompile it (yet).
Anyway, the options for small vendors/hobbyists are limited. If you use an unofficial VID/PID allocation, there is no guarantee it will be unique, but may work for most purposes, even getting a driver into the Windows driver database. If you want to go the official route, there is no option other than to integrate an FTDI product, with the limitations that entails, or purchase a vendor ID.
A while back, I've obtained a block of Product IDs from FTDI at no charge. I think it would be very advantageous to both Arduino LLC and small makers/vendors/hobbyists to have a similar option available.