USE_BOOST_HEADERS is incorrectly persistent

If you ever once issue a compilation command with -sUSE_BOOST_HEADERS, Boost somehow ends up on the include path of every subsequent compilation. This is unexpected and incorrect, as for example one might want to use a different version of Boost than what is included, leading to incompatibilities or confusing errors.

Reproducing minimal repo at: https://github.com/mmarczell-graphisoft/embug/commit/d846c9e4770e5cbc3645d62247753e9e2fca9c0e

Reproduction CI run at: https://github.com/mmarczell-graphisoft/embug/actions/runs/23202095356/job/67427039648#step:4:1

**Version of emscripten/emsdk:**
5.0.3

**Failing command line in full:**
```bash
em++ main.cpp # this fails, correctly
em++ -sUSE_BOOST_HEADERS main.cpp # this succeeds correctly
em++ main.cpp # this succeeds incorrectly
```