Your understanding is fully correct.
The LS1043ARDB schematics was prepared in assumption that twin-die DDD4 SDRAM devices can be used.
From the Micron Data Sheet:
"DDR4 will support a traditional DDP package, which uses these three signals for control of the second die (CS1_n, CKE1, ODT1)."
You wrote:
> For the two rank configuration, would the CS, ODT, and CKE [0] signals connect to the
> DRAM of Rank1 and the CS, ODT, and CKE [1] signals all connect to Rank2?
CS0, ODT0, CKE0 - rank 0 (1)
CS1, ODT1, CKE1 - rank 1 (2)