The bug was prior to the additional changes, but it would have still impacted crew on land. The correct prioritization is listed in the notes.
Crew on Land:
1st priority: Resource Box and Food larder
2nd priority: Silo
3rd priority: Claim Flags
Crew on Fully Anchored Boats:
1st priority: Silo
2nd priority: Claim Flags
3rd priority: Resource Box and Food larder
Additionally, with claimflags you can choose:
Not to use any gold or food to pay for your crew on your island
Have the gold/food only be used to pay for crew belonging to your company on your island
Have the gold/food only be used to pay for crew belonging to your company and allies on your island
Have the gold/food only be used to pay for crew belonging to your everyone on your island
I think that covers about everything, I am going to go ahead and lock this thread cause the back and forth is a bit needless