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When you use the EMAC HPS I/O pins as loaner I/O don't expect them to have to have many features. As you can see from the output there is no altddio atom in the HPS I/O. Loaner I/O do not have double data rate logic, delay chains, registers, etc... in them. Loaner I/O are intended to be use for low speed connectivity since the I/O is limited in functionality and the delay between two adjacent loaner I/O is much more than what you are accustom to with the regular FPGA I/O.
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Thanks BadOmen.