Zachary VIII said:
Spoilers for the canon Darth Vader comic series:
The clone biochips in canon are dumb. I’ve just read the Darth Vader comic and in it a Jedi uses Order 66 to make a clone squad turn on their Inquisitor leaders because they’re technically still in the list of Jedi. He just says “execute Order 66” and the clones start gunning down the Inquisitors. What the hell is that? Why is “Order 66” a magic spell that anyone can use now instead of only the Chancellor himself?
I’d assume because he (and probably Vader) were the only ones to know about the triggering phrase at that point. Most of the Jedi who heard it ended up dead, and Palpatine did end up replacing (most) clone troopers with recruits during the first couple of years of the Empire anyway.
I also can’t recall it ever being stated that the order had to come from Palaptine himself, which wouldn’t have made any sense as the Kaminoan’s didn’t know about Palpatine. I can’t remember the details, but a few high ranking Kaminoans were told it was a safeguard against rogue Jedi ordered by Sifo Dyas and Tyrannus/Dooku.
And the whole inhibitor chips thing did fail briefly during a Clone Wars arc, so it was never a foolproof method to begin with (probably because of all the secrecy around it). Basically the chips made them suddenly hate all Jedi, and since Sith and Inquisitor’s weren’t a thing when they were programmed into their brains, it makes sense that it’d give them an urge to kill anyone associated with the concept of “Jedi” in a generalized manner.
(Anyway, as with most PT/CW era ideas, it gets rather convoluted.)