eye powers intact=/=EMS abilities. it may also mean that he retained sharingan or MS techs. other than that, there's absolutely no clue that this madara dude has EMS right now.
If Madara did use Izanagi and went blind in his eyes, how can he use his Sharingan now? Does that mean Madara had to abduct an Uchiha ninja and transplant his eyes?
it is possible to use izanagi with only 1 eye too. so it is possible to use izanagi and sacrifice one eye and still retain the powers of the other eye, thus "eye powers are still intact" but not necessarily all. if EMS does requires a pair of eyes, then you'd probably lose EMS if you sacrifice one eye with izanagi.