To Run the Exchange Calendar update tool from one workstation: do I need to have separate runs for each timezone, such as one for Eastern, one for Central , one for Pacific changing the Admin Workstation to that time zone each time ?

Q: To Run the Exchange Calendar update tool from one workstation: do I need to have separate runs for each timezone, such as one for Eastern,  one for Central , one for Pacific changing the Admin Workstation to that time zone each time ?
A: No you can run rebasing from one specific machine only, tool takes care of it.

You should be ok, regardless you have multiple time zones in one file.