For clarity's sake: the Yuzu repository is most likely radioactive in general. As part of the settlement, the judge issued an injunction to declare Yuzu as software to exist solely to bypass TPMs. That gives Nintendo the legal right to issue takedowns (and pursue legal action) against Yuzu code. It doesn't set any precedent for other emulators though.

As far as I can tell, yes, injunctions like that extend beyond the person they've been issued against. Sure, it may not be fully correct assuming you modify the Yuzu code to take out everything to do with bypassing TPMs, but Nintendo has a strong legal team and the ability to drag out a court case if you want to test that. I don't think most people will want to do that.