Advantage of doing the USB method is that it will save your settings/drivers/etc. So if you can give it free space on the drive, do it.
Although, I don't know what will happen if your stick is less than 16GB. (TF2 is 12.2GB.)
Copy the TF2 gcf's from windows if you have it installed (then verify game cache) and you'll shave off like 80% of the download time on Linux. (In home folder show hidden files, then go into .steam then Steam then SteamApps for the folder in Linux.)