Actually, only the IVs are set permanently when you first encounter Thundurus/Tornadus. Nature and shininess can be reset upon defeating the Elite 4.
I have not personally RNG'd these 2, but I'm fairly certain that's how it works. So to answer the question, to get your desired nature just beat the E4 and then SR for it. Synchronizers don't work on them.
Anyways, roamers don't exist in BW2.