Actually, I think it's the other way around. A clone has all your files as files; a time machine backup is a single container. When you restore, you have options, including migration assistant (see the official Apple support pages on restore).
I know, because I restored from an external drive, not from a time machine back up (at first). I gave the store a machine with Lion, but they gave me back a machine with Mountain Lion. Since my time machine backup was made under Lion, it was invisible to Mountain Lion (at least it was not a choice given to me). I went ahead without thinking too much and restored from another external drive. I ended up with Mountain Lion as the OS with all my Snow Leopard apps on it, including all those that wouldn't run without rosetta. So can you restore from an external drive that holds actual files? Definitely.
So did I have to use my Lion install disk? No. Apple Care support had me boot into recovery, go to disk utilities, and wipe the drive. As soon as the wipe finished, it asked if I wanted to restore and time machine was an option. After my second restore, I had my Lion back.
You don't need to hold the option key. If you don't get the right choice, just restart and hold the option key, but I really don't think it will be necessary.