D is a project for a systems programming language with GC enabled by default. There a couple of experimental OSes like PowerNex.
RocksDB is not part of the Cassandra project, as far as I can tell.
Anyway it doesn't matter how niche they are, rather they were successful implemented and aren't mainstream as a consequence of politics and willingness to push it forward.
Doing UNIX clones is cheaper than improving the overall security.
Which is why in spite of the ergonic issues of using the NDK as it is, I enjoy the fact that Google makes it quite hard to use C and C++ instead of Java/Kotlin on Android.
Which on their little brother variant, Android Things, is even more explicit with user space drivers being written in Java.
Then we have Apple pushing Swift, which even if it takes another decade, it will eventually make Objective-C join Carbon.
Modern systems programming seems to be the land of luddites in IT.
https://fahrplan.events.ccc.de/congress/2018/Fahrplan/events...
https://www.infoq.com/presentations/csharp-systems-programmi...
D by Digital Mars is a language not a project.
The java use cases you mention seem very niche. Even databases written in Java ( Cassandra) started migrating a lot of parts to C++ (myrocks)
The Microsoft Research ones too don't seem like they came out of Microsoft Research to being used in shipped products.