No, you’re not the only one. I totally agree with you. It was stupid. In the Clone Wars Multimedia Project there wasn’t any chip, and it was done Better.
Unfortunately by living in Italy we had limited access to more niche SW literature, by the time TCW’s movie/series arrived they started catching up, but before it was a mess, i bought some republic commando and yuuzhan vong saga novels out of desperation one summer in 2006 when i went to the UK for vacation.
How did they put it in the multimedia project?
I’m Italian too and I understand you perfectly, in our country It’s very difficult to find Star Wars books, because publishers are lazy and never translate anything. Anyway, in the Multimedia Project the Clones were genetically engineered to obey every order without question, just as it’s established in Attack of the Clones, therefore 99.9% of regular Clones obeyed Order 66. However, Clones of higher rank such as Commandos and ARC troopers were more independent than regular Clones, and had the ability to disobey orders. It was necessary to make them more independent than regular Clones, because the kind of missions they were designed to participate in required more independence and free thinking. In fact, most of these Clones obeyed Order 66, but there were also many cases of desertion.