While there has been a change in how text is written to XML files in Java 9's XML framework (compared to the way text was written in Java 8 and earlier), yEd has been adjusted to this change since yEd version 3.17.2.
Indeed, using yEd 3.19.1.1 with Java 11.0.2, your single node example results in the following GraphML file:
<graphml ...>
<graph ...>
...
<node id="n0">
...
<y:ShapeNode>
...
<y:NodeLabel ... xml:space="preserve">This is centered<y:LabelModel>...</y:ModelParameter></y:NodeLabel>
...
</y:ShapeNode>
</data>
</node>
</graph>
...
</graphml>
Note the xml:space="preserve" attribute for the <y:NodeLabel> element.