Can God do whatever he wants?

Arguments from evil, divine hiddenness, "undesign", and so forth rely on something like the following general form:

1. The God of traditional theism has the omni-properties (i.e., omniscience, omnipotence, moral perfectionà commonly associated to Him
2. If the God of traditional theism exists, we expect that God would not allow for/bring about X (where X stands for hiddenness, evil, imperfection, animal suffering, a wasteful evolutionary process, ...) 
3. But X occurs 
4. Therefore, God doesn't have the omniproperties commonly associated to Him
5. Therefore, the God of traditional theism doesn't exist.

(Note that this argument as it stands is invalid. In order to be valid, (2) should be replaced with 2*. If the God of traditional theism exists, God would not allow for/bring about X, but this stronger version is more difficult to defend, since it would require some logical incompatibility between the omni-properties and things like evil and hiddenness.).

Premise 2 relies on our human intuitions vis à vis de compatibility of traditional theism with some properties of the world. There are two types of responses to these arguments

• Question the omni-properties (e.g., process theology, kenotic God)
• Provide a theodicy for why X occurs in spite of God having the omni-properties.

Notice, however, that the validity of (2) is rarely questioned. Yet, Sydney Penner (a specialist in medieval and early modern philosophy here at Oxford) pointed out to me that holding God under these kinds of moral, epistemic etc. obligations is a relatively recent development in philosophy. According to him, medieval philosophers did not place God under such obligations. Basically, God could do whatever he wanted. Although medieval theologians did consider evil and divine hiddenness, they did not accord the same weight to it as philosophers since the modern era. Early modern philosophers like Descartes, Leibniz and Hume were novel in their assumption that we can reasonably infer what God would or would not do, given the properties of theism (e.g., God wouldn't deceive us, because He's morally perfect). I am wondering if other specialists in medieval/early modern philosophy have the same intuition, and if so, if they could explain where this change came from.