No idea about tour operators arrangements, but the regular daily Bluestar ferry to Naxos and onwards is at 15:30, the last one of the day, except in last week July/August when there is another catamaran at 17:20.
For hotel you must check with the travel operator.
Depends very much on the tour operator and their arrangements. In the past they have chartered boats like the Naxos Star as well as use the domestic ferries to move people from islands with airports to islands without. These days I believe it is more common to use the local ferries.
A flight that lands a 1400 to meet a 1530 ferry does not leave much leeway in case of any delay. The ferry certainly will not wait for a delayed flight.
A friend booked 7 "nights" on Naxos a couple of years back on a package, and they ended up with one night travelling on the plane, and had to overnight on Mykonos both there and back due to ferry and flight times so only ended up with 4 actual nights on Naxos.
We have booked international flights to Athens to connect with internal Olympic flights to the island. There are 3 flights each way daily but they can get full during high season (we booked in October of last year!).
We are taking EasyJet from Manchester to Athens (an early morning flight) then the 4pm on to the island.
That might be a better option for you, then find your own accommodation?
Here is a link to a website I created last year http://makinw.wix.com/lessercyclades
There is a 'Getting There' button with info re the flights and ferries, and general and accommodation hints for Naxos itself. Hope you find it useful.
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