The enable semantic rules option (enableSemanticRules) appears to cause the linter to lint the previous versions of the file saved on disk, rather than the current contents of the editor. This is especially noticeable in atom-ide-ui which does not update the linting again on save, but is also noticeable in linter-ui-default as the linting does not update while typing.
GIF of the issue in atom-ide-ui:

Is this maybe what is meant by "May negatively affect performance"?
EDIT: I've figured out what's going on here, and detailed it below.