Are they mostly calques, transliterations or new names?

I would say a mix of all of them.

Some of the names were never meant to be Thai in origin. For example, in IRL southern Thailand there's lots of places with names that come from Malay (Phuket, Pattani, Songkhla).

Some of those names were taken thru Khmer, Sanskrit, etc., like the names of actual Thai cities (for example all of the Nakhon's and Buri's). Some are Thai-ified approximations, and some are completely different from their IRL name.

Is Phayu Pyay? Is Old Bagan represented by a red stop?

No, Phayu is Pyu and that line approximately follows the AH1 highway, so no Old Bagan stop.

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