Compensating for inaccuracies in Dafny's JSON logs

Dafny's logs don't report correctly some things. The bug is [known](https://github.com/dafny-lang/dafny/issues/5718#issuecomment-2306719989) and `log_readers` compensates for it. However, when it gets fixed upstream this will also need to be fixed in `log_readers`.