Nintendo owned the trademark for Star Twins, and they still do. That means they have the legal right to use the name in marketing. That's a huge difference, and not the same as owning the copyright, which is ostensibly the property in and of itself. That, like every other Rare created property, was kept by them in the transition to Microsoft.
Star Twins was a name that Nintendo had mandated when they published the game in Japan, so the trademark being theirs makes sense. Presumably the reason it was never applied by Microsoft was they either never intended to keep using that name, or it's just because it's a super low priority franchise. One thing to remember is that Rare was never an entirely owned subsidiary. Nintendo really only owned 49% of the company, so to a majority extent, most of the original creations Rare put out were in large part owned by themselves.
They wouldn't have retained trademarks for anything except Star Twins and Blast Dozer given that those were the titles that underwent name changes for Japanese publishing. Most likely Nintendo had trademarks for just about every other Rare franchise at some point (with the possible exception of Conker), but those were obviously given up because they were easy to track and not as esoteric or disposable.
That being said, I don't have any active links to those names on trademark databases. It's possible those trademarks have expired by now, but given their presence in the game's files, it's safe to assume they log their trademarks closely, and those two games appearing in Smash's files makes the most sense if any at all are present.