is there any logical difference between 我坐著公車 and 我在坐公車
我在坐公車 and 我坐著公車 have pretty similar meanings.
To emphasize ON THE BUS/PLANE/....
Q: 你在哪？我在坐公車。(I am on the bus NOW)
Q: 你在幹嘛？ A:我在坐飛機。(I am on the air plane NOW) Q: 坐飛機去哪？(Where are you flying to?) A: 去美國。
To emphasize other actions rather than (or related to) THE BUS/PLANE/....
我坐著飛機，到世界各國旅行。 (travel around the world by air plane)
我坐著交通船，每天家跟辦公室之間往來。我坐著交通船，每天在家跟辦公室之間往來。
我坐著火車，到海邊散散心。
我在坐飛機 could be translated "sitting in the plane"
Literally, yes, it looks like "sitting on the plane". But that should be realized with "ON THE AIR PLANE" rather than SITTING on the plane.
If you wish to emphasize the action of sitting, you can say 我在飛機上坐著.
boarding a plane
We usually use 登機 or 上飛機. e.g. If you see "登機中" at boarding gate, it means passengers are allowed to board a plane. When you are already on the plane, you can say 我在飛機上 我在坐飛機 我上飛機了。