Yeah, if you read $2000-$5FFF sequentially, it reads the 2nd half of the physical ROM first, and then the 1st half($2000-3FFF CPU A13=1, $4000-$5FFF CPU A13=0).

From a user point of view, sequential data file(easy to disasm) + emulator cross compatibility is nice. But if we're going to be purists, a 1:1 copy of the ROM chip is better.