This isn't really the case, though. Lots of options are completely orthogonal (e.g. tabs vs spaces and function brace style don't really affect each other). My experience with clang-format has been that each option (mostly) only affects a single token type, which is determined using clang as a backend. I've only seen satisfactory results.

If you don't have as powerful a backend as the full clang paraer/lexer on the other hand, I could quickly see things breaking as you described.