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They are still assigned under the hood by the linker. The magic is in the atari-cart.cfg file which tells the linker where the data segments go. For cartridges .SEGMENT "DATA" starts at $2000.

As for the actual register: The 6502 has them on the chip itself. They have no memory address at all.

That's great to know. I'll take a look at the 6502 datasheet. Time for me to learn about other 8-bit microprocessors.