Easy explanation: instead of Cut+Paste Itachi did Copy+Paste.

I don't see why Itachi would have had to lose his own abilities when he imbued them into Sasuke. Very little about this situation makes any sense right now. A 0 effort technique transfer is unprecedented in the series so trying to apply rules or boundaries to what may or may not have happened seems pointless.

I hope it turns out to be the case that Itachi used the chakra manipulation aspect of genjutsu to induce Mangekyou in Sasuke's eyes. An explanation like that would fit with what we already know about the Narutoverse and I would prefer not to have to swallow another pill of Deus ex Sharingan when a more generic explanation is viable as well.