And for what its worth, that is actually exactly what I do for native query execution via JPA... I flush the entire Session to be compliant with that exact sentiment. However even there I exposed the ability to specify synchronize-tables for the native query via hints. The reason being that it is much more performant generally speaking.

As I said I am not against that per-se. But I never like to hurt the performance of users that do the right thing to accommodate users that do not do the right thing. To me this is a (new - enhancement) setting that is disabled by default (current behavior)