'White House communications director Dan Bartlett said Bush did not take the physical because he was not going to be in a flying capacity in Alabama. "Those who are trying to read the mind of a person dead 20 years are stretching at best. The president at every turn did what he was told to do."'
I said it before and I'll say it again. Refusing to take a flight physical in the reserves/guard is not a prosecutable offense. It merely means one loses his/her qualification to fly. The 'orders' are not legally binding in the sense that they fall under the UCMJ. There is no dereliction of duty implicit in those actions.
Even on active duty, a person is not required to take a flight physical if he has chosen to give up his wings.
As for the CO's not wanting to rate an officer who has been drilling elsewhere, in the Navy we would call it an "NOB" (not observed) fitrep. They are given all the time. If Bush got a fitrep from his Alabama unit he wouldn't need one from Texas. And if he didn't get one at all, that's a problem only if he was hoping to get promoted. If he was leaving the service, missing a fitrep is absolutely meaningless.