What’s to stop him from giving clemency to the Blind Sheikh, if anything?
Yep he can pardon anyone he wants. There aren’t really any “rules”, only a current method by which is usually gets done. Which of course this instance proves all you need “is a pen and a phone”.
Regards the boats, they likely were in international waters and the current ROE/Obama house rules being what they are, instead of shooting their attackers, they surrender and a story is made up to “prove” that Iran was not making an act of war.