A "3" address from an Electrum 2FA wallet is a "2of3" MultiSig and actually has 3 private keys. 1 key is controlled by TrustedCoin (you need a Google Authenticator code to get them to sign a transaction), the other 2 keys are controlled by your "seed words". By default, 1 of these seed words keys is stored in the wallet file. This is the private key you get when you "export" the private key from Electrum.
The 2nd private key is only stored in your wallet if you restore it using your 2FA seed words and choose "DISABLE" when prompted to keep or disable 2FA functionality.
Any combination of 2 of these 3 private keys will be able to sign a transaction that is able to spend coins from the address. However, you will struggle to be able to recreate your "3" address in another wallet unless it allows creation of MultiSig Addresses and even then it won't be easy.
It does not matter which private key you use. All the private keys will work.