By sub-type variance are you referring to issues like this https://stackoverflow.com/questions/47850513/unsafe-implicit... ?

FWIW the lack of explicit variance annotations (and probably many other TS unsound design choices) are not so much related to supporting old untyped JS, but rather language design decisions that have to do with pragmatism and type system complexity.

I can't find it now but I have a vague recollection Hejlsberg talking about the explcit variance annotations explicitly, how those were a huge can of worms in C# and they didn't want to bring them to TS. Unlike Flow, by the way, which does have explicit variance handling and doesn't suffer from the beforementioned foot gun (but does have its own foot guns of course).