Hello CJO, and welcome to cruise-chat;
Tracy Arm is not an alternative itinerary to the Inside Passage; it is another place to view glaciers besides Glacier Bay.
There are basically two types of Alaskan itineraries: Inside Passage, which go round trip from Seattle, Vancouver or San Francisco; and those that cross the Bay of Alaska, either Northbound (usually Vancouver to Anchorage) or Southbound (the reverse).
Some visit Tracy Arm; others, Glacier Bay.
So there is some other factor in the price difference.
Prices for Alaska can vary greatly according to date-even on the same ship.
If you could give us some more information, ship, date, itinerary, I'm sure we can help you sort it all out.