On the first one, I'd say that I strongly agree that presidents can challenge the options they are given, but whether they will is another question. On the one hand, if there's one main lesson from Richard Neustadt's Presidential Power, it's that presidents should be active, not passive. On the other hand...Saunders is selecting the very highest stakes decisions, ones that both life and death and the future of the presidency are clearly at stake. It's one thing for a president to spend the time it takes to ask for additional options on that kind of decision; a president who does that for everything will rapidly run out of time. Dickinson's example was White House staff re-organization -- should Jimmy Carter really have spent more time on that? Perhaps so (given that his eventual choices weren't very good ones), but if that, then maybe not specific budget decisions, or choices about energy policy, or health care policy, or appointments, or, well, something. Presumably the art to this is to challenge the options presented often enough (and sharply enough) that those presenting the options get a good sense of the president's real preferences, and generally to keep everyone on their toes. But there are real limits, too.
On the second one, the problem is that (especially outside of the White House staff) presidential advisors have multiple bosses: not just the president, but their agency's bureaucracy, Congress, and perhaps outside groups. As Saunders says:
[T]he bureaucracy will surely leave its own mark on presidential options--whether through deliberate manipulation, well-intentioned but misguided advice, bad information, or flying under the radar of presidential monitoring.Now, she's certainly correct that "when we observe a president selecting from options presented to him by advisers, we cannot necessarily conclude that he had little effect on their formation." But that's a fairly minimal standard.
What I'd say, following Neustadt -- and the more I learn about presidents, the more I think he's right -- is that it's certainly possible for a president to amass a great deal of influence, both inside and outside of his administration. But that influence must be earned, every step of the way. It doesn't come with the job, and it doesn't come easily.