These keys are generated with Key #2 and you overwrute Key #2 with a garbage key to exploit this. So, while the keys are still set in the keyslots, you can't use themp, because they are garbage.KeyX is set by Arm9Loader and KeyY is set by NATIVE_FIRM, so I guess you are right since KeyX is probably already cleared by the time arm9loaderhax runs. If we could get the normal key somehow it would be possible, but that's probably not going to happen any time soon.
If you use memchunkhax2+ntrcardhax on sysNAND 9.6+, you will be able to use the keys (are they are set in keyslots), but not to know their values. Plus Nintendo will probably change the keys soon.