Currently how you get on the boat/ship (water) is different from the Air ship where you have to open up the menu rather than talking to the NPC to get in. Triairy replied with the following response.

Quote Originally Posted by Triairy View Post
こんばんは。
Good evening,

定期船と飛空艇の乗り場の仕様が違うことについては、開発チームでも認識しており、
パッチ1.22以降、定期船の乗り場の仕様を変更して、飛空艇乗り場の仕様に統一させる予定です。
The dev team also acknowledges that the method to get into boat/ship and air ship area is different. Post 1.22 we are planning to make changes so that the method to get inside boat/ship area will be changed and will be same as how you get on the air ship. (basically talking to the NPC)

フィードバックありがとうございました。
thanks for the feedback