What is Transit Station in Hyperdia

What in the world is "transit station" as appears on the timetable search in Hyperdia sometimes? Does it mean I have to change train?

For instance there is a JR Special Rapid Service Train from Shin-Osaka to Nagahama, where the transit stations are said to be Kyoto and Maibara. Until Maibara it says JR Special Rapid Service but after it changes to JR Hokuriku Line. I am confused...

And on the Ltd Exp Super Inaba (3) from Okayama to Tottori, Kamigori is a Transit Station, but same train name. Why do they put that as a transit station? It just makes confusion.

A yellow box that says "Tra." means that you will have to change trains at that station. Two downward pointing arrows mean that you do NOT have to transfer trains. The stations are shown for technical reasons because the train is running along different train lines. If you asked me, Hyperdia should get rid of them for user-friendliness.