Single "Multiple Inputs Tx" vs Multiple "Single Input Tx"
With option 2, most analyses will conclude that Alice owned A1, A2 and A3, because the transactions which spent them have no change address. Typically, you assume that the amount you have held in a TXO never exactly matches the amount you're making as a payment, so transactions usually have change outputs too.

I think you have a little misunderstanding about where bitcoins are held. Bitcoins are not stored in addresses. You don't "spend an address." You spend one or more UTXOs. Each transaction in option 2 creates a separate TXO, even though they share the same address for spending. This means, when the coins associated with A4 get spent in full, the individual TXOs are each inputs for the new transaction, which makes it look more like option 1 (multiple inputs, one output) when spent, like this.

+--------------------+
|A4 (txo1)         B1|
|A4 (txo2)   -&gt;      |
|A4 (txo3)           |
+--------------------+


Bob can of course, look at each of these inputs and see which transaction they came from, but he can't necessarily determine whether the addresses actually belonged to Alice, or whether it is just likely that is the case. Without some more evidence from further back in the history of the coins, you cannot prove whether Alice owned them initially or received them from somebody else.