You do have to pay seperately. Disney Magical Express is the complimentary shuttle between MCO and WDW. Shuttles between PC and either MCO or WDW are DCL transfers and for that you get to pay the $35/person each way.
No. As noted, the Magical Express is the (free) shuttle between MCO and WDW resorts.
Transportation between MCO and port; or WDW resorts and port; or port to either WDW resort/MCO is provided by DCL transportation. And it costs $35.00 per person for each leg.
The "Yes" I answered was in response to the OP's title post, "Does DCL transfer fee still apply if staying at Disney resort?" The answer to that is yes.
(May have been a tad confusing as the OP asked a different question within the post, not repeating the title question.)
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