First of all it wasn't me! I checked before replying.
Many of these flights operate with split loads, with some customers disembarking in JSI (Skiathos) and some in VOL (Nea Anchialos.) Which way around depends on timing factors and sometimes the aircraft that is utilized. The route is served by both 320/1 and B757 aircraft. The latters performance enables it to operate from the short runway at Skiathos directly back to the UK with less of a penalty restriction. However apron capacity at Skiathos will often put a practical restriction on which way around the flight is programmed.
Skiathos is a category C airport and landing and take off there is usually restricted to the captain. That said, Volos can be an awkward little airport for many of the reasons that have already been mentioned. ATC and ATC co-ordination often results in aircraft being very high when approaching the airfield. Topography and "valley effect winds" can have a significant influence. Thermals are also very prevalent and often give rise to turbulence on the approaches. From the description you give it sounds very much as if the pitching and rolling sensations you experienced where as a result of such turbulence.
I am not sure if the landing was smooth, felt like a 4.5 magnitude Earthquake, or possibly was the cause of it? But in any event, we have all been there and whilst everyone endeavours to kiss the ground where prudent, it doesn't always happen! On those rare (ahem) occasions when it has happened to me over the last 30 years, I used to tell the cabin crew that we avoided a family of baby ducks on the runway, and it thumped down as a result. You then went from villain to hero in 10 seconds! However now you mention the 4.5 magnitude Earthquake (and the duck story has worn a bit thin,) I might tuck that one away for future reference.