Presumably that at least allows him to break through any locks. Mastering this wandlessly will make it impossible to effectively restrain him while leaving conscious. The choice to make it possible is still on the author, because the Magic could make it impossible regardless, as it holds lots of conceptual knowledge already and can impose map distinctions of its own, however the wizard conceptualizes the situation.
Presumably that at least allows him to break through any locks. Mastering this wandlessly will make it impossible to effectively restrain him while leaving conscious. The choice to make it possible is still on the author, because the Magic could make it impossible regardless, as it holds lots of conceptual knowledge already and can impose map distinctions of its own, however the wizard conceptualizes the situation.
Unless the restraints are protected against transfiguration.
If the ability to transform just portions of objects is completely novel, those protections might or might not extend to it.
In other words: rejoice, Eliezer! Whichever you choose will be plausible! (As long as you remember to be consistent)
If you can prevent apparition by powerful wizards you can quite likely prevent transfiguration via a similar mechanism.