Your first sentence is implying a single possibility : he already left the island and his boat sunk in the ocean. Your second formulation would imply 2 exclusive possibilities using an enumeration of “Et si … ?”, which is kinda illogical and would sound weird. You would also use “avait” instead of “a” in the second formulation.

Concerning the punctuation in the first formulation, the question mark is used to suggest an in-progress spoken/thought process : what if XXX? (pause to think) And then YYY would have happened. Using the second formulation you lose this effect and instead you are considering both possibilities independantly, trying to put them in opposition (either one or the other but not both).

The first sentance is equivalent to :

Et si il avait déjà quitté l’île, et que son bateau ait coulé quelque part au milieu de l’océan ?

But it implies the speaker made an hypothesis and ended his sentence. Then, he thought of something else (something even worse!) and added it. The sentence is imperfect, but it shows the train of thought of the speaker. Or it could be to make two short sentences instead of a long one.

The reason why "ait" is used instead of "avait" is that "que" requires the use of a subjonctive in this case.

Finally, two “si”s change the meaning of the sentence. Here is an example :

Et si la souris était sortie de son trou ? Et qu’elle se soit fait manger.

What if the mouse had gone out ? And had been eaten [outside]. (A=>B)?

It is different than :

Et si la souris était sortie de son trou ? Et si elle s’était fait manger ?

What if the mouse had gone out ? What if it had been eaten [inside or outside its hole]. (A? B?)