That's not really what's going on here. "Ninjutsu OS" is a modified Windows 10 ISO. Basically a pirated copy.
You are right, they were distributing a modified version of Windows without permission. And there's nothing notable or interesting about that. It's a pretty clear-cut case of "don't do that".
But ALSO.. the language in the MS/BSA complaint states that tools that help the user disable Windows 10 OS features - some that arguably benefit MS more than the user - run afoul of the DMCA's anti-circumvention clauses, and that's a much broader statement that has nothing to do with an uploaded ISO.
If this stands, does it mean that I am not allowed to use similar tools to disable features on my legit copy of Windows 10? That's what the language in their complaint implies.
does that matter? You can put whatever you want on a DMCA complaint. It's not going to be subject to any judicial review. I wouldn't be worried unless they actually initiate a lawsuit.