@Chris Cranford You are correct that this only affects the 5.2.x release stream. I do not know what I did wrong previously, but I am sorry for any confusion I may have caused by stating that it affects previous versions.
As for the the section 4.6.4.1 of the JPA spec, you are also correct - but only for JPQL. For NamedNativeQueries the bug still stands. (See section 3.10.13 of the spec:

It is assumed that for native queries the parameters themselves use the SQL syntax (i.e., “?”, rather than “?1”).

)

This means that this bug is smaller in scope than I previously thought. But using 0-based for NamedNativeQueries is definitely incorrect.