Trying to disable position increments via SetEnablePositionIncrements(false) has no effect, at least on phrase queries.
The parsed query returned from the QueryParser with this input, should by default return a phrase query whose terms look like: "Query with Stopwords" should look silmilar to this if converted to a string: "query ? stopwords", where ? is a null term query in the phrase query.
With EnablePositionIncrements set to false, the resulting query should be similary to "query stopwords". However, calling SetEnablePositionIncrements(false) has no effect on the resulting query.