Thinking about this some more, I do not think either will work for our needs. Part of what we need to do is to also transform our tests also to test the main artifact that we transformed.
In other words, we need to transform both the hibernate-core main classes and test classes to use the Jakarta APIs and be able to run both set of tests (transformed and un-transformed). We need to make sure the transformation worked properly. I have not seen any capability like that in Gradle, at least built-in. Granted, this is a quite special situation (though certainly not unique as all libraries using Java EE will need a similar transformation in the coming year or 2).