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I don't have any experience with the Teensy but it looks like it has preloaded a bootloader called HalfKay. Unless you want to turn the Teensy into an Arduino it shouldn't matter which bootloader you use. The key differences is the Arduino bootloader and platform are designed to run over a serial port or virtual serial port. HalfKay, and Atmel's own DFU bootloaders are designed to run straight over USB.
Ultimately it changes what utility you can use to upload something, though if you want to use the Arduino platform I think you need to load the Arduino bootloader on the chip.
You can't change the bootloaders without an In-System-Programmer the whole purpose of the bootloader is that is loaded as No-Read-While-Write memory, meaning that the chip shuts down if the bootloader attempts to write itself. So don't count on changing bootloaders unless you have the programming hardware to do it.
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