When using <set-tx-query-timeout>true</set-tx-query-timeout, the query timeout is applied, unless less than 1 second remains until transaction timeout.

This is due to a typo in code converting transaction timeout (millis) into jdbc timeout (seconds).
Widlfy 9.0.2 uses IronJacama 1.2.5, so here's the code (https://github.com/ironjacamar/ironjacamar/blob/ironjacamar-1.2.5.Final/adapters/src/main/java/org/jboss/jca/adapters/jdbc/WrapperDataSource.java#L207):

            long result = timeout / 1000;
            if ((result % 1000) != 0) // <------   the `timeout % 1000` was supposed to be
               ++result;