Suite A is fairly specialised. Nobody can publicly comment on specific use cases of course, but it's fairly well known that Suite B is used for most national security information, including TS/SCI. But yes, technically non-public algorithms exist and are in use, it's just not even nearly automatically applied to everything.
Cool! It would be fascinating to read more about the Suite A ciphers and compare them to known designs, see how they were inspired by, improved or differ. But I guess there's not much chance of that happening as they're classified, haha! :)
They're using fips like the rest of govt. i get that you don't know. That's fine, but when you start making up stuff to fill in the gap that's when you need to do a reality check.