Correct. Apple had to make a really tough call on this one in my opinion. Basically they wrote the backup routine once and tied it to a set of conditions.
The key condition for both is the problem. "Connecting the phone to the charger" is what triggers either backup to start. Since Apple likes to keep it simple they didn't write it to do one back up and then the other. I am willing to bet a lot of people wish they had.
The other condition that makes it slightly problematic is recovering the phone in case of an issue. Remember when you setup a new iPhone under iOS 5, you can sign in with your iCloud account. The moment you do that, it triggers off the recovery process if it sees you had full backup turned on. But what if they gave you both options? And the back up you want is on iTunes because the last iCloud back up is where the data got corrupted? Now they would have to write even more code to deal with that possibility and handing control back to iTunes.
This is where Apple's philosophies of "Keep it simple" and "It just works" clash with users that are far more advanced than the average user that buys their product.