The shadar-kai were popular enough to warrant an update, and the elf-recon is to reconcile the playable 4e version with the fey-monster 3e one. Moreover, I don't believe Mystara will even warrant a mention in MToF. Its not a well-known or beloved setting except to a small subset of Basic-edition players who are too busy celebrating the RC being POD than caring about Tome of Foes. Mystara, it seems to the current design team, is a neat place to borrow things from (Isle of Dread, tortles, nagpa, rakasta...er tabaxi) but not a setting that warrants actual development.
Well, dusk elves in Curse of Strahd were already mentioned to be equivalent to wood elves, so I doubt that will be the case either.
And the SCAG said to use regular elves for sea, averiel and other kinds of elves. Things change when they have the space and opportunity to update them better.
So yeah in CofS they were a variantion of Wood Elves, as a place holder, they didn't want to introduce a new playable subrace in CofS. They do however want to do so in MTOFs.
Merging Dusk Elves, 3e Shadar Kai, and 4e Shadar Kai is EXACTLY HOW THEY CAME UP WITH 5E SHADAR KAI.
The Dusk Elves were Elves that refused to take sides between Corellon and Lloth and ended up cast into the Shadowfell for it.
The 5e Shadar Kai were Elves that refused to take sides in the War between Corellon and Lloth, it was because of this they ultimately became Shadar Kai, abit their fall was caused by the Raven Queen and the Nagpa, not Corellon getting mad and deeldarinifying them like the original Dusk Elves.
They share the shadowfell in common already, they were both the neutral faction in the war between Lloth and Corellon. Wood elves were just a mechanical place holder, like they were for Sea Elves, Avariel, Lythari, Wild Elves, ect... in the SCAG.
On one side High Elves, Wood Elves, Wild Elves, Sea Elves, Avierel, Lycanthari, Eldarin ect..., on the other Drow, Driders, Dreagloth, and maybe at times Fey'ri. The Shadar Kai aka Dusk Elves stand apart and are the Neutral side, they are at War (well generally, the Netheril War during the Sundering is an exception) with neither side and are willing to deal with either.
Still I believe they are more likely to use white drow for Shadow Elves then Shadar Kai anyways, because they are more tied to the underdark/hollow world then Shadar Kai usually are. Plus Drow have Suppiorior Darkvision as did Shadow Elves. Culturally they will be different for obvious reasons.