Amber Cove can only host 2 ships, the other two are scheduled for Puertp Plata, cruisemapper doesn't differentiate between the two, it just lumps them together.
Cruising on any given line is a choice. If you don't like what a cruise line is doing with charges, then pick a different one. They all do the same things but don't let that influence your decision.
Getting to Jost from St. Thomas can be done but it is not easy you have to have passport and clear customs and immigration both ways. In addition it is a pretty long ride. The ferries don't go to White Bay on Jost but into "town" so you would then have to walk over the hill or get a cab to Soggy Dollar.
Your best bet would be to charter a boat from Tortola and go that way.
You maybe able to get an upgrade, but the price of your cabin has not decreased so there is nothing to reduce. your best bet will be to upgrade to a higher category cabin that costs more than you paid and pay the difference.
There is no telling what you might end up with, but it is reasonable to assume that you will not be non stop from Tampa, and could layover almost anywhere.
If NCL books your flights don't make any assumption that you will get a non stop, in fact you are likely to have at least one connection. they are not good at booking for convenience.
Your airfare is set when you book. NCL may pay more or less what they charge you but you know the fare when you book the cruise. You will find out your flight information between 30 and 45 days before sailing.