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The ferry does mean less miles cycled. It's faster not to use the ferry, but for the people who aren't aiming to win it's one option that helps get a big block of sleep in mid-ride.
Rivoli to Vukovar =~ 1200km (avoiding motorways)
Rivoli to Ancona =~ 590km
Split to Vukovar =~ 430km(I picked Rivoli as most people went through it anyway)
So that ferry saves ~180km, but it's an 10h45 crossing, which is why it's faster to cycle.
Ferry = sleep.