Replacement for SDRAM controller after V16.1?

You are correct. But now you would use one of the UniPHY based IPs instead of the old SDRAM controller IP. They're even listed there in the screenshot you posted. Start here for information on EMIF solutions and documentation:

https://www.intel.com/content/www/us/en/programmable/support/literature/lit-external-memory-interface.html

The Design Guidelines handbook shows you how to add and parameterize the newer IP:

https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/hb/external-memory/emi_plan.pdf

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