Showing your passport in a nation like Israel, to prove your citizenship in order to receive treatment as a citizen, is different from traveling on your passport.
Yes . . . The issuing country has a say over how you use your local passport but the US government has the say over how you travel while holding a clearance. They want to be able to know where you are and where you are going.
Are you really going to use 20 year old travel to support the use of passports today? Twenty years ago, I could carry a case of shampoo in my carryon bag with having anything questioned but my sanity.