Will depend on what achievements you’re trying to get. But if say you want something that’s Vanquisher difficulty if you change deer to Pioneer, raiders to Trailblazer then yes, achievements won’t trigger. Everything in Advanced has to be Vanquisher setting if you want to get Vanquisher achievements. Originally it would only work if you chose Advanced at the main screen, but was changed in a hotfix.
I expect if you wanted Trailblazer and turned one or two things up to Vanquisher that would mean they don’t trigger either.
And using Custom Settings means achievements won’t trigger at all.