Creating an object from Magnolia's configuration calls different mechanisms depending on the way of instantiating it. Performing a manual instantiation calls Map2Bean while Magnolia handles it with Node2Bean.
However, it seems like Map2Bean is ignoring the class property when converting the configuration structure to their respective beans.
Bean created by Magnolia automatically:
Bean created via code:
Here we can see that the map is taking the class property as another value instead of assigning such value to the map type itself.
Attached is a simple filter class to reproduce the issue, along two configuration files that help reproduce it as well.