Right now Linter has some very basic code to highlight the spot of specific errors: https://phabricator.wikimedia.org/source/mediawiki-extensions-Linter/browse/master/modules/ext.linter.edit.js however this isn't compatible with VisualEditor.
Somehow we should have the &lintId= parameter always force the new source editor (or old source editor) instead of VE and then have our highlighting system work.