Are there security tradeoffs to be considered in deciding between encrypting an entire flashdrive with TrueCrypt versus storing a file encrypted container? The security goal is to be immune to the problem that wear leveling can store data on unused areas of the flash drive, so that all the encrypted data remains secure if the flash drive is lost.

If the entire device is encrypted, then the flash drive is useless without installing TrueCrypt. If a file container is used, then an unencrypted portion could still be used for other purposes (understanding that wear leveling could leave traces of those files), but does that create any vulnerability for the file encrypted portion?

Note that I understand that neither approach solves the problem of file fragments being left elsewhere in the system, e.g. in a swap file, without encrypting the entire system - that's not my question.