I would agree to large extent that the plugin is less accurate than the standard FDTD: the plugin uses simple stair case approximation at the material interface, whereas the standard FDTD can be more accurate. Please refer to https://optics.ansys.com/hc/en-us/articles/360034915213-Flexible-Material-Plugin-Framework
The signal is not that important, as long as your result is in frequency-domain. As your images show the intensity is quite similar, which indicates that your code is correct.
You may try finer mesh size and see if it improves. In addition, thicker slab can be better than the thinner slab as the interface cells are fewer for thick slab.
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Please also refer to the following Yee mesh to understand why the material interface is important:
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