I’ve already gotten far enough away from the book that the fx series encourages doubt on my interpretation of things, but I took away (from the book, mind you) that Toranaga saw Mariko and Anjin as subordinates but capable of understanding him and his plans, basically how he saw the world. Everyone else was held captive to tradition and custom.
He’s not amused by Anjin, rather he appreciates his insight, his expertise as a navigator, and because he’s a foreigner (and not welcome anywhere in Japan), he’s basically the only person he can have a heart to heart with and not feel like it’s at risk of being used against him. Plus, he knows about Mariko’s affection for him and that’s confirmation of his judgment.
The book doesn’t make him a heel; he’s the only one capable of imposing order in Japan and he’s willing to sacrifice his loyalists if it furthers that goal. In the book’s world he’s just holding Mariko back from dying so that her death can serve a greater purpose and she seems to understand this.
I don’t recall a bargain with the Portuguese to burn the boat (I may just be misremembering it), rather, he burned it because Anjin’s friendship was important to him and it was the only way to keep him from leaving (in the subtle, Japanese elite way of navigating conflict).