The purpose of TM and option key bootable clones is as a backup system.
Encrypting TM I perhaps can understand as it's connected to the machine all the time for the file recovery option.
But the clone should remain unencrypted so not only can you boot from it, but also access your files direclty in case it wont boot or unlock.
If you have to place the clone in a safe, then do so. A thief is going to take everything he see's anyway, if it's encrypted or not as they are after the hardware value.
If you have sensitive data, it should be stored on a self encrypting external hard drive or USB key, off the computer, these drives have their own hardware based encryption with a key or keypad, thus they can be taken to any computer and used to read the files.
Software based encryption is flaky and prone to being comprimised. Hardware based encrpytion is more secure as it can't be changed and requires a electornics specialist to crack it.
If your computer has a problem that it needs servicing and you can't boot to remove sensitive files, Apple will require the Filevault password to service it and they will see those files.
If you take the encrpted computer/anything through Customs, they can require your password and image your drive.
If your house gets raided by the police, they will demand the password(s) take the computer and anything else to search for evidence.
On top of all that, encrpyting the entire boot drive makes it difficult to "fix" in times of trouble and it slows down the performance.
https://discussions.apple.com/docs/DOC-3045
https://discussions.apple.com/community/notebooks/macbook_pro?view=documents