I do not get the information about the thicknesses of the two slabs and the source in experiment. However when both FDTD and RCWA give very similar result, but different from experiment, then you may need to consider the effect of coherence. I believe the thickness of each layer is very large, on the scale of 100um or more.
FDTD gives pure, single wavelength in coherent way. It does not consider any incoherence or partial coherece. However in experiment, if you do not use laser source, for example, you use nature light or florescent light or other incoherent sources, they are incoherent thus the ripples are averaged out. that is, the measured result is like this
where W is the spectral weight of the source. More information maybe found here https://optics.ansys.com/hc/en-us/articles/360034383074-Understanding-temporal-incoherence-in-FDTD
You can use stackrt to verify the FDTD/RCWA result: stackrt - Script command
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