NO, its not just fuel-its also port+hi-season surcharge, and if needed any bed/accomm. Rian reported that they have now also invented a special passholder surcharge.

The free ride is only with Greek 6-islands Pass.

There are many more ferries doing IT-GR and there may very well be another one thats cheaper in the end in price to pay-the shorter the trip, the lower the fare in general.

It may be the same charge as the high season surcharge or replace that charge. They don't specify in their booking module on superfast.com what charge it is but it only appears when you indicate you have a global pass. The amount varies (I've seen 7€ and 22€) but it is never 0 when you indicate a global pass.

Whenever I’ve tried applying the Global Pass I only get 30 percent off of the total price- it doesn’t mention anything about a high season surcharge. Is there a way to apply the Global Pass so that all I’m paying for is the fuel and high-season surcharge? 

You select "Interrail global pass” from the list of discounts. The high season price with this discount seems to be 42€ currently for Bari - Patras, when you choose a deck passage.

Hello, I realize that this answer is too late to be useful, but just in case other travelers had the same question: The 100% discount is only applicable to the Greek Island pass and not to regular Global/One Country passes. Global pass holders only receive a 30% discount. Please note that you do not have use a travel day when traveling by ferry with the 30% discount. You only need to use a travel day for this ferry when using the Greek Island pass. 

There isn’t an option to select ‘interrail global pass’ from the list - just the greek pass. Any ideas why this might be?

Sure there is:

But if you're under 26, it's better to book via www.anek.gr, since Superfast doesn't let you choose an Interrail or Eurail global pass if you're under 26.