Since orders in Aurora are sequential, the new refueling rules seem to imply that total time alongside during a port stay would be refueling plus cargo operations, overhauls, etc.
However, it's not clear why replenishing bunker shouldn't happen concurrently with cargo operations, replenishment of stores, minor hot works, etc. In fact, that is how most commercial vessels today operate.
A cleaner solution would be to have a general "port stay" order with options for which activities to perform, and then have those activities being performed concurrently (unless they are mutually exclusive - you probably have to do overhauls and cargo operations sequentially). No idea how much bother it would be to code, but something similar already exists for loading ground units, so I'm guessing it should be feasible.