I think I will have to change my view of the Opportunity Cost for the items acquired or obtained during the preparation, even when such items are usually available.
In the video by Modiphius team (Modiphius Plays: Star Trek Adventures - Part 1), the PCs actually buy the pattern enhancers for the Opportunity Cost even during the preparation on their ship before the away mission.
Such would indicated the Opportunity Cost had been meant to be paid even when there is a possibility to prepare.