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There would be no need to switch to EMS if Rinnegan could cast Genjutsu. Enough fanfiction.

Rinne-Sharingan, which we know has the powers of both Dojutsu, was used to cast Genjutsu. If tomoe-less Rinnegan could use Sharingan abilities then there would be no point for Tomoe Rinnegan and Rinne-Sharingan.

As you said, he used it even without eyes so what makes you think he specifically used it with his Rinnegan? His use of it isn't dependant on the eyes so there's no telling that he used his eyes for it when he had them. And even if he did, that's one ability. With Genjutsu he needed to switch.

Madara mastered the Rinnegan which is why he was able to teach Obito it's abilities. Normal Rinnegan can't use Sharingan abilities like the Tomoe Rinnnegan and Rinne-Sharingan. Which is why he switched to EMS to cast Genjutsu on Ay.

Tomoe-less Rinnegan can't use Sharingan abilities.