In order to generate 6.0.0+ savedata, a KeyY initialized by the NATIVE_FIRM version 10833 or newer is used. That key is initialized using a RSA keyslot, itself initialized by the bootrom.
The RSA keyslot is cleared when a CXI is loaded, this means that on a system where an older revision of NATIVE_FIRM was loaded by the bootrom, the keyY keyslot isn't loaded and the key required to generate the final KeyY stored in the RSA keyslot has been cleared long before your own code is running (therefore, long before 6.0.0+ NATIVE_FIRM is running from emuNAND)
This means the KeyY used on emuNAND 6.0.0. NATIVE_FIRM to generate the new 6.0.0+ savedata will always be different to the one used on 6.0.0 NATIVE_FIRM run from sysNAND. There is nothing, short of running code on a live 6.0.0. system BEFORE a CXI is loaded (this means early in the boot process), that can get you the real key.