The inhibitor chip ensures that Clone Troopers of the GAR will unquestioningly execute Order 66 when it is given, denying them free will in that crucial moment. How does it do it though? More specifically, does the chip execute its function via temporary mind control or a permanent change to their brains?
The implications are that, for the former, the clones will eventually regain full control of themselves, thereafter realising what they have done and will most probably regret their actions since, in such a case, the Jedi's trust in their loyalty are not unfounded in a sense. For the latter, I feel that there may be various ways it is achieved. The chip may either permanently override the clone's brain, taking control for life, or it may reconfigure the clone's brain altogether, such that while the clone is still in full control of himself, he is literally no longer the same person he was prior to the Order.
As such, how the inhibitor chip executes its intended functionality affects the nature of the chip's design and how it is implemented.